From 2899031b71578da690b37c44fa58804564f39e3a Mon Sep 17 00:00:00 2001 From: Vitor Hideyoshi Nakazone Batista Date: Thu, 17 Jun 2021 20:01:42 -0300 Subject: [PATCH] v0.0.1 Signed-off-by: Vitor Hideyoshi --- .control.in.swp | Bin 0 -> 12288 bytes DPpack/Dice.py | 534 +++++ DPpack/Gaussian.py | 420 ++++ DPpack/Misc.py | 63 + DPpack/MolHandling.py | 603 ++++++ DPpack/Molcas.py | 348 ++++ DPpack/Optimization.py | 266 +++ DPpack/PTable.py | 35 + DPpack/SetGlobals.py | 813 ++++++++ DPpack/__init__.py | 0 DPpack/__pycache__/Dice.cpython-36.pyc | Bin 0 -> 12358 bytes DPpack/__pycache__/Misc.cpython-36.pyc | Bin 0 -> 1655 bytes DPpack/__pycache__/MolHandling.cpython-36.pyc | Bin 0 -> 13551 bytes DPpack/__pycache__/PTable.cpython-36.pyc | Bin 0 -> 2363 bytes DPpack/__pycache__/SetGlobals.cpython-36.pyc | Bin 0 -> 16816 bytes DPpack/__pycache__/__init__.cpython-36.pyc | Bin 0 -> 152 bytes .../__pycache__/mol_handling.cpython-36.pyc | Bin 0 -> 6254 bytes control.in | 21 + diceplayer-0.0.1.py | 295 +++ geoms.xyz | 33 + ghosts.in | 6 + lps.in | 4 + new_cyclo.xyz | 1602 +++++++++++++++ new_cyclo.xyz.new | 1602 +++++++++++++++ new_cyclo.xyz.new2 | 1782 +++++++++++++++++ othercontrol.in | 11 + phb.pot | 51 + phb.xyz.last-p01 | 1633 +++++++++++++++ phb.xyz.last-p02 | 1633 +++++++++++++++ run.log | 229 +++ test4.py | 64 + 31 files changed, 12048 insertions(+) create mode 100644 .control.in.swp create mode 100644 DPpack/Dice.py create mode 100644 DPpack/Gaussian.py create mode 100644 DPpack/Misc.py create mode 100644 DPpack/MolHandling.py create mode 100644 DPpack/Molcas.py create mode 100644 DPpack/Optimization.py create mode 100644 DPpack/PTable.py create mode 100644 DPpack/SetGlobals.py create mode 100644 DPpack/__init__.py create mode 100644 DPpack/__pycache__/Dice.cpython-36.pyc create mode 100644 DPpack/__pycache__/Misc.cpython-36.pyc create mode 100644 DPpack/__pycache__/MolHandling.cpython-36.pyc create mode 100644 DPpack/__pycache__/PTable.cpython-36.pyc create mode 100644 DPpack/__pycache__/SetGlobals.cpython-36.pyc create mode 100644 DPpack/__pycache__/__init__.cpython-36.pyc create mode 100644 DPpack/__pycache__/mol_handling.cpython-36.pyc create mode 100644 control.in create mode 100644 diceplayer-0.0.1.py create mode 100644 geoms.xyz create mode 100644 ghosts.in create mode 100644 lps.in create mode 100644 new_cyclo.xyz create mode 100644 new_cyclo.xyz.new create mode 100644 new_cyclo.xyz.new2 create mode 100644 othercontrol.in create mode 100644 phb.pot create mode 100644 phb.xyz.last-p01 create mode 100644 phb.xyz.last-p02 create mode 100644 run.log create mode 100644 test4.py diff --git a/.control.in.swp b/.control.in.swp new file mode 100644 index 0000000000000000000000000000000000000000..cef465e8d7959097d29e0ab400b862602829943b GIT binary patch literal 12288 zcmeI2v2N5b7{|XNF#-i7HbiLWyCm0^!q5Rx2{9CPpof6T=L<<7u}$J@n*mth6?gzv zUVtZHXJ%((;sy9Sq(Wji=0pETKRchl&vx?LqIi}}9~?xx<88sUE>ceKK6!TUq3G)( zh0ZhE4a+Nar<e_VNI;9@r|v< zrTO>5te^oJSZ-k9pO0=|INF+|NhsXhxEWo&a63OeE=(*O<701eOp z4bT7$&;Sk401d2|fhs%Bs%S4dIGn_4k&m<)vKif1i?%Hl&YIhWH>%E1<%*e9 zFa88$XT6lIIu6M+NfI%w&m4kn1W9zOZ+Ai~^USnJB;(zkNK9?Ru4$NrNZTe0$rSs} zaqeA2RX(f~1}FXWys)hgp|Mi+(49uSB?cMYPZ#SvhPtek UTAiNdOM~jZHjRc|f1kFOUynkAdH?_b literal 0 HcmV?d00001 diff --git a/DPpack/Dice.py b/DPpack/Dice.py new file mode 100644 index 0000000..33889a6 --- /dev/null +++ b/DPpack/Dice.py @@ -0,0 +1,534 @@ +import sys, os, time +import subprocess + +from copy import deepcopy + +from numpy import random + +from DPpack.PTable import * +from DPpack.SetGlobals import * +from DPpack.Misc import * + + +dice_end_flag = "End of simulation" ## The normal end flag +dice_flag_line = -2 ## must be in the line before the last +umaAng3_to_gcm3 = 1.6605 ## Conversion between uma/Ang3 to g/cm3 + +max_seed = 4294967295 ## Maximum allowed value for a seed (numpy) + +####################################### functions ###################################### + +def make_inputs(cycle, proc): + + step_dir = "step{:02d}".format(cycle) + proc_dir = "p{:02d}".format(proc) + path = step_dir + os.sep + proc_dir + + num = time.time() ## Take the decimal places 7 to 12 of the + num = (num - int(num)) * 1e6 ## time in seconds as a floating point + num = int((num - int(num)) * 1e6) ## to make an integer in the range 1-1e6 + random.seed( (os.getpid() * num) % (max_seed + 1) ) + + if not dice['randominit']: + xyzfile = dice['outname'] + ".xyz.last-" + "p{:02d}".format(proc) + make_init_file(path, xyzfile) + + if len(dice['nstep']) == 2: ## Means NVT simulation + + make_nvt_ter(path) + make_nvt_eq(path) + + elif len(dice['nstep']) == 3: ## Means NPT simulation + + if dice['randominit']: + make_nvt_ter(path) + else: + dice['dens'] = new_density(proc) + + make_npt_ter(path) + make_npt_eq(path) + + else: + sys.exit("Error: bad number of entries for 'nstep'") + + make_potential(path) + + return + + +def make_nvt_ter(path): + + file = path + os.sep + "NVT.ter" + try: + fh = open(file, "w") + except: + sys.exit("Error: cannot open file {}".format(file)) + + fh.write("title = {} - NVT Thermalization\n".format(dice['title'])) + fh.write("ncores = {}\n".format(dice['ncores'])) + fh.write("ljname = {}\n".format(dice['ljname'])) + fh.write("outname = {}\n".format(dice['outname'])) + + string = " ".join(str(x) for x in dice['nmol']) + fh.write("nmol = {}\n".format(string)) + + fh.write("dens = {}\n".format(dice['dens'])) + fh.write("temp = {}\n".format(dice['temp'])) + + if dice['randominit']: + fh.write("init = yes\n") + fh.write("nstep = {}\n".format(dice['nstep'][0])) + else: + fh.write("init = yesreadxyz\n") + fh.write("nstep = {}\n".format(player['altsteps'])) + + fh.write("vstep = 0\n") + fh.write("mstop = 1\n") + fh.write("accum = no\n") + fh.write("iprint = 1\n") + fh.write("isave = 0\n") + fh.write("irdf = 0\n") + + seed = int(1e6 * random.random()) + fh.write("seed = {}\n".format(seed)) + + fh.close() + + return + + +def make_nvt_eq(path): + + file = path + os.sep + "NVT.eq" + try: + fh = open(file, "w") + except: + sys.exit("Error: cannot open file {}".format(file)) + + fh.write("title = {} - NVT Production\n".format(dice['title'])) + fh.write("ncores = {}\n".format(dice['ncores'])) + fh.write("ljname = {}\n".format(dice['ljname'])) + fh.write("outname = {}\n".format(dice['outname'])) + + string = " ".join(str(x) for x in dice['nmol']) + fh.write("nmol = {}\n".format(string)) + + fh.write("dens = {}\n".format(dice['dens'])) + fh.write("temp = {}\n".format(dice['temp'])) + fh.write("init = no\n") + fh.write("nstep = {}\n".format(dice['nstep'][1])) + fh.write("vstep = 0\n") + fh.write("mstop = 1\n") + fh.write("accum = no\n") + fh.write("iprint = 1\n") + fh.write("isave = {}\n".format(dice['isave'])) + fh.write("irdf = {}\n".format(10 * player['nprocs'])) + + seed = int(1e6 * random.random()) + fh.write("seed = {}\n".format(seed)) + + fh.close() + + return + + +def make_npt_ter(path): + + file = path + os.sep + "NPT.ter" + try: + fh = open(file, "w") + except: + sys.exit("Error: cannot open file {}".format(file)) + + fh.write("title = {} - NPT Thermalization\n".format(dice['title'])) + fh.write("ncores = {}\n".format(dice['ncores'])) + fh.write("ljname = {}\n".format(dice['ljname'])) + fh.write("outname = {}\n".format(dice['outname'])) + + string = " ".join(str(x) for x in dice['nmol']) + fh.write("nmol = {}\n".format(string)) + + fh.write("press = {}\n".format(dice['press'])) + fh.write("temp = {}\n".format(dice['temp'])) + + if dice['randominit']: + fh.write("init = no\n") ## Because there will be a previous NVT simulation + fh.write("vstep = {}\n".format(int(dice['nstep'][1] / 5))) + else: + fh.write("init = yesreadxyz\n") + fh.write("dens = {:<8.4f}\n".format(dice['dens'])) + fh.write("vstep = {}\n".format(int(player['altsteps'] / 5))) + + fh.write("nstep = 5\n") + fh.write("mstop = 1\n") + fh.write("accum = no\n") + fh.write("iprint = 1\n") + fh.write("isave = 0\n") + fh.write("irdf = 0\n") + + seed = int(1e6 * random.random()) + fh.write("seed = {}\n".format(seed)) + + fh.close() + + return + + +def make_npt_eq(path): + + file = path + os.sep + "NPT.eq" + try: + fh = open(file, "w") + except: + sys.exit("Error: cannot open file {}".format(file)) + + fh.write("title = {} - NPT Production\n".format(dice['title'])) + fh.write("ncores = {}\n".format(dice['ncores'])) + fh.write("ljname = {}\n".format(dice['ljname'])) + fh.write("outname = {}\n".format(dice['outname'])) + + string = " ".join(str(x) for x in dice['nmol']) + fh.write("nmol = {}\n".format(string)) + + fh.write("press = {}\n".format(dice['press'])) + fh.write("temp = {}\n".format(dice['temp'])) + + fh.write("nstep = 5\n") + + fh.write("vstep = {}\n".format(int(dice['nstep'][2] / 5))) + fh.write("init = no\n") + fh.write("mstop = 1\n") + fh.write("accum = no\n") + fh.write("iprint = 1\n") + fh.write("isave = {}\n".format(dice['isave'])) + fh.write("irdf = {}\n".format(10 * player['nprocs'])) + + seed = int(1e6 * random.random()) + fh.write("seed = {}\n".format(seed)) + + fh.close() + + return + + +def make_init_file(path, file): + + if not os.path.isfile(file): + sys.exit("Error: cannot find the xyz file {} in main directory".format(file)) + try: + with open(file) as fh: + xyzfile = fh.readlines() + except: + sys.exit("Error: cannot open file {}".format(file)) + + nsites_mm = 0 + for i in range(1, len(dice['nmol'])): + nsites_mm += dice['nmol'][i] * len(molecules[i]) + + nsites_mm *= -1 ## Become an index to count from the end of xyzfile (list) + xyzfile = xyzfile[nsites_mm :] ## Only the MM atoms of the last configuration remains + + file = path + os.sep + dice['outname'] + ".xy" + + try: + fh = open(file, "w") + except: + sys.exit("Error: cannot open file {}".format(file)) + + for atom in molecules[0]: + fh.write("{:>10.6f} {:>10.6f} {:>10.6f}\n".format(atom['rx'], atom['ry'], + atom['rz'])) + + for ghost in ghost_atoms: + fh.write("{:>10.6f} {:>10.6f} {:>10.6f}\n".format(ghost['rx'], ghost['ry'], + ghost['rz'])) + + for lps in lp_atoms: + fh.write("{:>10.6f} {:>10.6f} {:>10.6f}\n".format(lps['rx'], lps['ry'], + lps['rz'])) + + for line in xyzfile: + atom = line.split() + rx = float(atom[1]) + ry = float(atom[2]) + rz = float(atom[3]) + fh.write("{:>10.5f} {:>10.5f} {:>10.5f}\n".format(rx, ry, rz)) + + fh.write("$end") + + fh.close() + + return + + +def make_potential(path): + + fstr = "{:<3d} {:>3d} {:>10.5f} {:>10.5f} {:>10.5f} {:>10.6f} {:>9.5f} {:>7.4f}\n" + + file = path + os.sep + dice['ljname'] + try: + fh = open(file, "w") + except: + sys.exit("Error: cannot open file {}".format(file)) + + fh.write("{}\n".format(dice['combrule'])) + fh.write("{}\n".format(len(dice['nmol']))) + + nsites_qm = len(molecules[0]) + len(ghost_atoms) + len(lp_atoms) + + ## Print the sites of the QM molecule + fh.write("{}\n".format(nsites_qm)) + for atom in molecules[0]: + fh.write(fstr.format(atom['lbl'], atom['na'], atom['rx'], atom['ry'], atom['rz'], + atom['chg'], atom['eps'], atom['sig'])) + + ghost_label = molecules[0][-1]['lbl'] + 1 + for ghost in ghost_atoms: + fh.write(fstr.format(ghost_label, ghost_number, ghost['rx'], ghost['ry'], + ghost['rz'], ghost['chg'], 0, 0)) + + ghost_label += 1 + for lp in lp_atoms: + fh.write(fstr.format(ghost_label, ghost_number, lp['rx'], lp['ry'], lp['rz'], + lp['chg'], 0, 0)) + + ## Print the sites of the other molecules + for mol in molecules[1:]: + fh.write("{}\n".format(len(mol))) + for atom in mol: + fh.write(fstr.format(atom['lbl'], atom['na'], atom['rx'], atom['ry'], + atom['rz'], atom['chg'], atom['eps'], atom['sig'])) + + return + + +def make_proc_dir(cycle, proc): + + step_dir = "step{:02d}".format(cycle) + proc_dir = "p{:02d}".format(proc) + path = step_dir + os.sep + proc_dir + try: + os.makedirs(path) + except: + sys.exit("Error: cannot make directory {}".format(path)) + + return + + + +def run_dice(cycle, proc, fh): + + step_dir = "step{:02d}".format(cycle) + proc_dir = "p{:02d}".format(proc) + path = step_dir + os.sep + proc_dir + working_dir = os.getcwd() + os.chdir(path) + + fh.write("Simulation process {} initiated with pid {}\n".format(proc_dir, os.getpid())) + + if len(dice['nstep']) == 2: ## Means NVT simulation + + ## NVT thermalization + string = "(from " + ("random" if dice['randominit'] else "previous") + " configuration)" + fh.write("p{:02d}> NVT thermalization initiated {} on {}\n".format(proc, string, + date_time())) + + infh = open("NVT.ter") + outfh = open("NVT.ter.out", "w") + + exit_status = subprocess.call(dice['progname'], stdin=infh, stdout=outfh) + infh.close() + outfh.close() + + if os.getppid() == 1: ## Parent process is dead + sys.exit() + + if exit_status != 0: + sys.exit("Dice process p{:02d} did not exit properly".format(proc)) + else: + outfh = open("NVT.ter.out") ## Open again to seek the normal end flag + flag = outfh.readlines()[dice_flag_line].strip() + outfh.close() + if flag != dice_end_flag: + sys.exit("Dice process p{:02d} did not exit properly".format(proc)) + + ## NVT production + fh.write("p{:02d}> NVT production initiated on {}\n".format(proc, date_time())) + + infh = open("NVT.eq") + outfh = open("NVT.eq.out", "w") + + exit_status = subprocess.call(dice['progname'], stdin=infh, stdout=outfh) + infh.close() + outfh.close() + + if os.getppid() == 1: ## Parent process is dead + sys.exit() + + if exit_status != 0: + sys.exit("Dice process p{:02d} did not exit properly".format(proc)) + else: + outfh = open("NVT.eq.out") ## Open again to seek the normal end flag + flag = outfh.readlines()[dice_flag_line].strip() + outfh.close() + if flag != dice_end_flag: + sys.exit("Dice process p{:02d} did not exit properly".format(proc)) + + fh.write("p{:02d}> ----- NVT production finished on {}\n".format(proc, + date_time())) + + elif len(dice['nstep']) == 3: ## Means NPT simulation + + ## NVT thermalization if randominit + if dice['randominit']: + string = "(from random configuration)" + fh.write("p{:02d}> NVT thermalization initiated {} on {}\n".format(proc, + string, date_time())) + infh = open("NVT.ter") + outfh = open("NVT.ter.out", "w") + + exit_status = subprocess.call(dice['progname'], stdin=infh, stdout=outfh) + infh.close() + outfh.close() + + if os.getppid() == 1: ## Parent process is dead + sys.exit() + + if exit_status != 0: + sys.exit("Dice process p{:02d} did not exit properly".format(proc)) + else: + outfh = open("NVT.ter.out") ## Open again to seek the normal end flag + flag = outfh.readlines()[dice_flag_line].strip() + outfh.close() + if flag != dice_end_flag: + sys.exit("Dice process p{:02d} did not exit properly".format(proc)) + + ## NPT thermalization + string = (" (from previous configuration) " if not dice['randominit'] else " ") + fh.write("p{:02d}> NPT thermalization initiated{}on {}\n".format(proc, string, + date_time())) + infh = open("NPT.ter") + outfh = open("NPT.ter.out", "w") + + exit_status = subprocess.call(dice['progname'], stdin=infh, stdout=outfh) + infh.close() + outfh.close() + + if os.getppid() == 1: ## Parent process is dead + sys.exit() + + if exit_status != 0: + sys.exit("Dice process p{:02d} did not exit properly".format(proc)) + else: + outfh = open("NPT.ter.out") ## Open again to seek the normal end flag + flag = outfh.readlines()[dice_flag_line].strip() + outfh.close() + if flag != dice_end_flag: + sys.exit("Dice process p{:02d} did not exit properly".format(proc)) + + ## NPT production + fh.write("p{:02d}> NPT production initiated on {}\n".format(proc, date_time())) + + infh = open("NPT.eq") + outfh = open("NPT.eq.out", "w") + + exit_status = subprocess.call(dice['progname'], stdin=infh, stdout=outfh) + infh.close() + outfh.close() + + if os.getppid() == 1: ## Parent process is dead + sys.exit() + + if exit_status != 0: + sys.exit("Dice process p{:02d} did not exit properly".format(proc)) + else: + outfh = open("NPT.eq.out") ## Open again to seek the normal end flag + flag = outfh.readlines()[dice_flag_line].strip() + outfh.close() + if flag != dice_end_flag: + sys.exit("Dice process p{:02d} did not exit properly".format(proc)) + + fh.write("p{:02d}> ----- NPT production finished on {}\n".format(proc, + date_time())) + + os.chdir(working_dir) + + return + + + +def print_last_config(cycle, proc): + + step_dir = "step{:02d}".format(cycle) + proc_dir = "p{:02d}".format(proc) + path = step_dir + os.sep + proc_dir + file = path + os.sep + dice['outname'] + ".xyz" + if not os.path.isfile(file): + sys.exit("Error: cannot find the xyz file {}".format(file)) + try: + with open(file) as fh: + xyzfile = fh.readlines() + except: + sys.exit("Error: cannot open file {}".format(file)) + + nsites = ( len(molecules[0]) + len(ghost_atoms) + len(lp_atoms) ) * dice['nmol'][0] + for i in range(1, len(dice['nmol'])): + nsites += dice['nmol'][i] * len(molecules[i]) + + nsites += 2 ## To include the comment line and the number of atoms (xyz file format) + + nsites *= -1 ## Become an index to count from the end of xyzfile (list) + xyzfile = xyzfile[nsites :] ## Take the last configuration + + + file = dice['outname'] + ".xyz.last-" + proc_dir + fh = open(file, "w") + for line in xyzfile: + fh.write(line) + + fh.close() + + return + + + +def new_density(proc): + + file = dice['outname'] + ".xyz.last-" + "p{:02d}".format(proc) + if not os.path.isfile(file): + sys.exit("Error: cannot find the xyz file {} in main directory".format(file)) + try: + with open(file) as fh: + xyzfile = fh.readlines() + except: + sys.exit("Error: cannot open file {}".format(file)) + + box = xyzfile[1].split() + volume = float(box[-3]) * float(box[-2]) * float(box[-1]) + + total_mass = 0 + for i in range(len(molecules)): + mol_mass = 0 + for atom in molecules[i]: + mol_mass += atom['mass'] + total_mass += mol_mass * dice['nmol'][i] + + density = (total_mass / volume) * umaAng3_to_gcm3 + + return density + + + +def simulation_process(cycle, proc, logfh): + + try: + make_proc_dir(cycle, proc) + make_inputs(cycle, proc) + run_dice(cycle, proc, logfh) + except Exception as err: + sys.exit(err) + + return + + + diff --git a/DPpack/Gaussian.py b/DPpack/Gaussian.py new file mode 100644 index 0000000..5871a0e --- /dev/null +++ b/DPpack/Gaussian.py @@ -0,0 +1,420 @@ +import os, sys +import textwrap +import subprocess + +from DPpack.PTable import * +from DPpack.SetGlobals import * +from DPpack.MolHandling import * +from DPpack.Misc import * + +####################################### functions ###################################### + +def read_forces_fchk(file, fh): + + forces = [] + try: + with open(file) as tmpfh: + fchkfile = tmpfh.readlines() + except: + sys.exit("Error: cannot open file {}".format(file)) + + start = fchkfile.pop(0).strip() + while start.find("Cartesian Gradient") != 0: ## expression in begining of line + start = fchkfile.pop(0).strip() + + degrees = 3 * len(molecules[0]) + count = 0 + while True: + values = fchkfile.pop(0).split() + forces.extend([ float(x) for x in values ]) + count += len(values) + if count >= degrees: + forces = forces[:degrees] + break + + gradient = np.array(forces) + + fh.write("\nGradient read from file {}:\n".format(file)) + fh.write("-----------------------------------------------------------------------\n" + "Center Atomic Forces (Hartree/Bohr)\n" + "Number Number X Y Z\n" + "-----------------------------------------------------------------------\n") + for i in range(len(molecules[0])): + fh.write(" {:>5d} {:>3d} {:>14.9f} {:>14.9f} {:>14.9f}\n".format( + i + 1, molecules[0][i]['na'], forces.pop(0), forces.pop(0), forces.pop(0))) + + fh.write("-----------------------------------------------------------------------\n") + + force_max = np.amax(np.absolute(gradient)) + force_rms = np.sqrt(np.mean(np.square(gradient))) + + fh.write(" Max Force = {:>14.9f} RMS Force = {:>14.9f}\n\n".format( + force_max, force_rms)) + + return gradient + + + +def read_hessian_fchk(file): + + force_const = [] + try: + with open(file) as tmpfh: + fchkfile = tmpfh.readlines() + except: + sys.exit("Error: cannot open file {}".format(file)) + + start = fchkfile.pop(0).strip() + while start.find("Cartesian Force Constants") != 0: + start = fchkfile.pop(0).strip() + + degrees = 3 * len(molecules[0]) + last = round(degrees * (degrees + 1) / 2) + count = 0 + while True: + values = fchkfile.pop(0).split() + force_const.extend([ float(x) for x in values ]) + count += len(values) + if count >= last: + force_const = force_const[:last] + break + + hessian = np.zeros((degrees, degrees)) + for i in range(degrees): + for j in range(i + 1): + hessian[i,j] = force_const.pop(0) + hessian[j,i] = hessian[i,j] + + return hessian + + + +def read_hessian_log(file): + + try: + with open(file) as tmpfh: + logfile = tmpfh.readlines() + except: + sys.exit("Error: cannot open file {}".format(file)) + + start = logfile.pop(0).strip() + while start.find("The second derivative matrix:") != 0: + start = logfile.pop(0).strip() + + degrees = 3 * len(molecules[0]) + hessian = np.zeros((degrees, degrees)) + + k = 0 + while k < degrees: + logfile.pop(0) + for i in range(k, degrees): + values = logfile.pop(0).split()[1:] + for j in range(k, min(i + 1, k + 5)): + hessian[i,j] = float(values.pop(0)) + hessian[j,i] = hessian[i,j] + k += 5 + + return hessian + + + +def print_grad_hessian(cycle, cur_gradient, hessian): + + try: + fh = open("grad_hessian.dat", "w") + except: + sys.exit("Error: cannot open file grad_hessian.dat") + + fh.write("Optimization cycle: {}\n".format(cycle)) + fh.write("Cartesian Gradient\n") + degrees = 3 * len(molecules[0]) + for i in range(degrees): + fh.write(" {:>11.8g}".format(cur_gradient[i])) + if (i + 1) % 5 == 0 or i == degrees - 1: + fh.write("\n") + + fh.write("Cartesian Force Constants\n") + last = degrees * (degrees + 1) / 2 + count = 0 + for i in range(degrees): + for j in range(i + 1): + count += 1 + fh.write(" {:>11.8g}".format(hessian[i,j])) + if count % 5 == 0 or count == last: + fh.write("\n") + + fh.close() + + return + + + +def make_force_input(cycle, asec_charges): + + path = "step{:02d}".format(cycle) + os.sep + "qm" + file = path + os.sep + "asec.gjf" + try: + fh = open(file, "w") + except: + sys.exit("Error: cannot open file {}".format(file)) + + fh.write("%Chk=asec.chk\n") + if gaussian['mem'] != None: + fh.write("%Mem={}MB\n".format(gaussian['mem'])) + fh.write("%Nprocs={}\n".format(player['nprocs'] * dice['ncores'])) + + kword_line = "#P " + gaussian['level'] + " " + gaussian['keywords'] + kword_line += " Force Charge NoSymm" + + if cycle >= player['switchcyc']: + kword_line += " Pop={} Density=Current".format(gaussian['pop']) + + if cycle > 1: + kword_line += " Guess=Read" + + fh.write(textwrap.fill(kword_line, 90)) + fh.write("\n") + + fh.write("\nForce calculation - Cycle number {}\n".format(cycle)) + fh.write("\n") + fh.write("{},{}\n".format(gaussian['chgmult'][0], gaussian['chgmult'][1])) + + for atom in molecules[0]: + symbol = atomsymb[atom['na']] + fh.write("{:<2s} {:>10.5f} {:>10.5f} {:>10.5f}\n".format(symbol, + atom['rx'], atom['ry'], atom['rz'])) + + ## If also performing charge fit in the same calculation + if cycle >= player['switchcyc']: + for ghost in ghost_atoms: + fh.write("Bq {:>10.5f} {:>10.5f} {:>10.5f}\n".format( + ghost['rx'], ghost['ry'], ghost['rz'])) + + for lp in lp_atoms: + fh.write("Bq {:>10.5f} {:>10.5f} {:>10.5f}\n".format( + lp['rx'], lp['ry'], lp['rz'])) + + fh.write("\n") + + ## If gmiddle file was informed, write its contents in asec.gjf + if gaussian['gmiddle'] != None: + if not os.path.isfile(gaussian['gmiddle']): + sys.exit("Error: cannot find file {} in main directory".format( + gaussian['gmiddle'])) + try: + with open(gaussian['gmiddle']) as gmiddlefile: + gmiddle = gmiddlefile.readlines() + except: + sys.exit("Error: cannot open file {}".format(gaussian['gmiddle'])) + + for line in gmiddle: + fh.write(line) + + fh.write("\n") + + ## Write the ASEC: + for charge in asec_charges: + fh.write("{:>10.5f} {:>10.5f} {:>10.5f} {:>11.8f}\n".format( + charge['rx'], charge['ry'], charge['rz'], charge['chg'])) + + fh.write("\n") + + ## If gbottom file was informed, write its contents in asec.gjf + if gaussian['gbottom'] != None: + if not os.path.isfile(gaussian['gbottom']): + sys.exit("Error: cannot find file {} in main directory".format( + gaussian['gbottom'])) + try: + with open(gaussian['gbottom']) as gbottomfile: + gbottom = gbottomfile.readlines() + except: + sys.exit("Error: cannot open file {}".format(gaussian['gbottom'])) + + for line in gbottom: + fh.write(line) + + fh.write("\n") + + fh.close() + + return + + + +def make_charge_input(cycle, asec_charges): + + path = "step{:02d}".format(cycle) + os.sep + "qm" + file = path + os.sep + "asec2.gjf" + try: + fh = open(file, "w") + except: + sys.exit("Error: cannot open file {}".format(file)) + + fh.write("%Chk=asec.chk\n") + if gaussian['mem'] != None: + fh.write("%Mem={}MB\n".format(gaussian['mem'])) + fh.write("%Nprocs={}\n".format(player['nprocs'] * dice['ncores'])) + + kword_line = "#P " + gaussian['chglevel'] + " " + gaussian['keywords'] + " Charge NoSymm" + + if player['opt'] != "no" or cycle > 1: + kword_line += " Guess=Read" + + kword_line += " Pop={} Density=Current\n".format(gaussian['pop']) + + fh.write(textwrap.fill(kword_line, 90)) + fh.write("\n") + + fh.write("\nCharge calculation - Cycle number {}\n".format(cycle)) + fh.write("\n") + fh.write("{},{}\n".format(gaussian['chgmult'][0], gaussian['chgmult'][1])) + + for atom in molecules[0]: + symbol = atomsymb[atom['na']] + fh.write("{:<2s} {:>10.5f} {:>10.5f} {:>10.5f}\n".format(symbol, + atom['rx'], atom['ry'], atom['rz'])) + + if cycle >= player['switchcyc']: + for ghost in ghost_atoms: + fh.write("Bq {:>10.5f} {:>10.5f} {:>10.5f}\n".format( + ghost['rx'], ghost['ry'], ghost['rz'])) + + for lp in lp_atoms: + fh.write("Bq {:>10.5f} {:>10.5f} {:>10.5f}\n".format( + lp['rx'], lp['ry'], lp['rz'])) + + fh.write("\n") + + ## If gmiddle file was informed, write its contents in asec.gjf + if gaussian['gmiddle'] != None: + if not os.path.isfile(gaussian['gmiddle']): + sys.exit("Error: cannot find file {} in main directory".format( + gaussian['gmiddle'])) + try: + with open(gaussian['gmiddle']) as gmiddlefile: + gmiddle = gmiddlefile.readlines() + except: + sys.exit("Error: cannot open file {}".format(gaussian['gmiddle'])) + + for line in gmiddle: + fh.write(line) + + fh.write("\n") + + ## Write the ASEC: + for charge in asec_charges: + fh.write("{:>10.5f} {:>10.5f} {:>10.5f} {:>11.8f}\n".format( + charge['rx'], charge['ry'], charge['rz'], charge['chg'])) + + fh.write("\n") + + ## If gbottom file was informed, write its contents in asec.gjf + if gaussian['gbottom'] != None: + if not os.path.isfile(gaussian['gbottom']): + sys.exit("Error: cannot find file {} in main directory".format( + gaussian['gbottom'])) + try: + with open(gaussian['gbottom']) as gbottomfile: + gbottom = gbottomfile.readlines() + except: + sys.exit("Error: cannot open file {}".format(gaussian['gbottom'])) + + for line in gbottom: + fh.write(line) + + fh.write("\n") + + fh.close() + + return + + + +def read_charges(file, fh): + + try: + with open(file) as tmpfh: + glogfile = tmpfh.readlines() + except: + sys.exit("Error: cannot open file {}".format(file)) + + start = glogfile.pop(0).strip() + while start != "Fitting point charges to electrostatic potential": + start = glogfile.pop(0).strip() + + glogfile = glogfile[3:] ## Consume 3 more lines + + fh.write("\nAtomic charges:\n") + fh.write("------------------------------------\n") + for atom in molecules[0]: + line = glogfile.pop(0).split() + atom_str = line[1] + charge = float(line[2]) + atom['chg'] = charge + fh.write(" {:<2s} {:>10.6f}\n".format(atom_str, charge)) + + if gaussian['pop'] == "chelpg": + for ghost in ghost_atoms: + line = glogfile.pop(0).split() + atom_str = line[1] + charge = float(line[2]) + ghost['chg'] = charge + fh.write(" {:<2s} {:>10.6f}\n".format(atom_str, charge)) + + for lp in lp_atoms: + line = glogfile.pop(0).split() + atom_str = line[1] + charge = float(line[2]) + lp['chg'] = charge + fh.write(" {:<2s} {:>10.6f}\n".format(atom_str, charge)) + + fh.write("------------------------------------\n") + + return + + + +def run_gaussian(cycle, type, fh): + + path = "step{:02d}".format(cycle) + os.sep + "qm" + work_dir = os.getcwd() + os.chdir(path) + + if type == "force": + infile = "asec.gjf" + elif type == "charge": + infile = "asec2.gjf" + + fh.write("\nCalculation of {}s initiated with Gaussian on {}\n".format(type, date_time())) + + exit_status = subprocess.call([player['qmprog'], infile]) + + if exit_status != 0: + sys.exit("Gaussian process did not exit properly") + + fh.write("Calculation of {}s finished on {}\n".format(type, date_time())) + + os.chdir(work_dir) + + return + + + +def run_formchk(cycle, fh): + + path = "step{:02d}".format(cycle) + os.sep + "qm" + work_dir = os.getcwd() + os.chdir(path) + + fh.write("Formatting the checkpoint file... ") + + exit_status = subprocess.call(["formchk", "asec.chk"]) + + fh.write("Done\n") + + os.chdir(work_dir) + + return + + + diff --git a/DPpack/Misc.py b/DPpack/Misc.py new file mode 100644 index 0000000..77a67fa --- /dev/null +++ b/DPpack/Misc.py @@ -0,0 +1,63 @@ +import os, sys, time +import shutil, gzip + +####################################### functions ###################################### + +def weekday_date_time(): + + return time.strftime("%A, %d %b %Y at %H:%M:%S") + + +def date_time(): + + return time.strftime("%d %b %Y at %H:%M:%S") + + +def compress_files_1mb(path): + + working_dir = os.getcwd() + os.chdir(path) + + files = filter(os.path.isfile, os.listdir(os.curdir)) + for file in files: + if os.path.getsize(file) > 1024 * 1024: ## If bigger than 1MB + filegz = file + ".gz" + try: + with open(file, 'rb') as f_in: + with gzip.open(filegz, 'wb') as f_out: + shutil.copyfileobj(f_in, f_out) + except: + sys.exit("Error: cannot compress file {}".format(file)) + + os.chdir(working_dir) + + return + + +def make_step_dir(cycle): + + step_dir = "step{:02d}".format(cycle) + if os.path.exists(step_dir): + sys.exit("Error: a file or directory {} already exists".format(step_dir)) + try: + os.makedirs(step_dir) + except: + sys.exit("Error: cannot make directory {}".format(step_dir)) + + return + + + +def make_qm_dir(cycle): + + step_dir = "step{:02d}".format(cycle) + path = step_dir + os.sep + "qm" + try: + os.makedirs(path) + except: + sys.exit("Error: cannot make directory {}".format(path)) + + return + + + diff --git a/DPpack/MolHandling.py b/DPpack/MolHandling.py new file mode 100644 index 0000000..6c8a447 --- /dev/null +++ b/DPpack/MolHandling.py @@ -0,0 +1,603 @@ +import sys, math +import textwrap +from copy import deepcopy + +import numpy as np +from numpy import linalg + +from DPpack.PTable import * +from DPpack.SetGlobals import * + + +####################################### functions ###################################### + +def center_of_mass(molecule): + + com = np.zeros(3) + total_mass = 0.0 + for atom in molecule: + total_mass += atom['mass'] + position = np.array([atom['rx'], atom['ry'], atom['rz']]) + com += atom['mass'] * position + + com = com / total_mass + + return com + + + +def center_of_mass_distance(molecule1, molecule2): + + com1 = center_of_mass(molecule1) + com2 = center_of_mass(molecule2) + dx = com1[0] - com2[0] + dy = com1[1] - com2[1] + dz = com1[2] - com2[2] + distance = math.sqrt(dx**2 + dy**2 + dz**2) + + return distance + + + +def center_of_mass_to_origin(molecule): + + com = center_of_mass(molecule) + for atom in molecule: + atom['rx'] -= com[0] + atom['ry'] -= com[1] + atom['rz'] -= com[2] + + return + + + +def charges_and_dipole(molecule): + + eA_to_Debye = 1/0.20819434 + charge = 0 + dipole = np.zeros(3) + for atom in molecule: + position = np.array([ atom['rx'], atom['ry'], atom['rz'] ]) + dipole += atom['chg'] * position + charge += atom['chg'] + + dipole *= eA_to_Debye + total_dipole = math.sqrt(dipole[0]**2 + dipole[1]**2 + dipole[2]**2) + + return [charge, dipole[0], dipole[1], dipole[2], total_dipole] + + + +def distances_between_atoms(molecule): + + distances = [] + dim = len(molecule) + for atom1 in molecule: + if atom1['na'] != ghost_number: + for atom2 in molecule: + if atom2['na'] != ghost_number: + dx = atom1['rx'] - atom2['rx'] + dy = atom1['ry'] - atom2['ry'] + dz = atom1['rz'] - atom2['rz'] + distances.append(math.sqrt(dx**2 + dy**2 + dz**2)) + + return np.array(distances).reshape(dim, dim) + + + +def eixos(molecule): + + eixos = np.zeros(3) + if len(molecule) == 2: + position1 = np.array([ molecule[0]['rx'], molecule[0]['ry'], molecule[0]['rz'] ]) + position2 = np.array([ molecule[1]['rx'], molecule[1]['ry'], molecule[1]['rz'] ]) + eixos = position2 - position1 + eixos /= linalg.norm(eixos) + elif len(molecule) > 2: + position1 = np.array([ molecule[0]['rx'], molecule[0]['ry'], molecule[0]['rz'] ]) + position2 = np.array([ molecule[1]['rx'], molecule[1]['ry'], molecule[1]['rz'] ]) + position3 = np.array([ molecule[2]['rx'], molecule[2]['ry'], molecule[2]['rz'] ]) + v1 = position2 - position1 + v2 = position3 - position1 + v3 = np.cross(v1, v2) + v2 = np.cross(v1, v3) + v1 /= linalg.norm(v1) + v2 /= linalg.norm(v2) + v3 /= linalg.norm(v3) + eixos = np.array([[v1[0], v1[1], v1[2]], + [v2[0], v2[1], v2[2]], + [v3[0], v3[1], v3[2]]]) + + return eixos + + + +def inertia_tensor(molecule): + + com = center_of_mass(molecule) + Ixx = Ixy = Ixz = Iyy = Iyz = Izz = 0.0 + for atom in molecule: + #### Obtain the displacement from the center of mass + dx = atom['rx'] - com[0] + dy = atom['ry'] - com[1] + dz = atom['rz'] - com[2] + #### Update the diagonal components of the tensor + Ixx += atom['mass'] * (dy**2 + dz**2) + Iyy += atom['mass'] * (dz**2 + dx**2) + Izz += atom['mass'] * (dx**2 + dy**2) + #### Update the off-diagonal components of the tensor + Ixy += atom['mass'] * dx * dy * -1 + Ixz += atom['mass'] * dx * dz * -1 + Iyz += atom['mass'] * dy * dz * -1 + + return np.array([[Ixx, Ixy, Ixz], + [Ixy, Iyy, Iyz], + [Ixz, Iyz, Izz]]) + + + +def minimum_distance(molecule1, molecule2): + + distances = [] + for atom1 in molecule1: + if atom1['na'] != ghost_number: + for atom2 in molecule2: + if atom2['na'] != ghost_number: + dx = atom1['rx'] - atom2['rx'] + dy = atom1['ry'] - atom2['ry'] + dz = atom1['rz'] - atom2['rz'] + distances.append(math.sqrt(dx**2 + dy**2 + dz**2)) + + return min(distances) + + + +def nearest_image(refmol, molecule, lx, ly, lz, criterium="com"): + + if criterium != "com" and criterium != "min": + sys.exit("Error in value passed to function nearest_image") + min_dist = 1e20 + for i in range(-1, 2): + for j in range(-1, 2): + for k in range(-1, 2): + + tr_vector = [i * lx, j * ly, k * lz] + new_molecule = translate(molecule, tr_vector) + if criterium == "com": + dist = center_of_mass_distance(refmol, new_molecule) + else: + dist = minimum_distance(refmol, new_molecule) + + if dist < min_dist: + min_dist = dist + nearestmol = deepcopy(new_molecule) + + return min_dist, nearestmol + + + +def calculate_step(gradient, hessian, fh): + + invhessian = linalg.inv(hessian) + pre_step = -1 * np.matmul(invhessian, gradient.T).T + maxstep = np.amax(np.absolute(pre_step)) + factor = min(1, player['maxstep']/maxstep) + step = factor * pre_step + + fh.write("\nCalculated step:\n") + pre_step_list = pre_step.tolist() + + fh.write("-----------------------------------------------------------------------\n" + "Center Atomic Step (Bohr)\n" + "Number Number X Y Z\n" + "-----------------------------------------------------------------------\n") + for i in range(len(molecules[0])): + fh.write(" {:>5d} {:>3d} {:>14.9f} {:>14.9f} {:>14.9f}\n".format( + i + 1, molecules[0][i]['na'], + pre_step_list.pop(0), pre_step_list.pop(0), pre_step_list.pop(0))) + + fh.write("-----------------------------------------------------------------------\n") + + fh.write("Maximum step is {:>11.6}\n".format(maxstep)) + fh.write("Scaling factor = {:>6.4f}\n".format(factor)) + fh.write("\nFinal step (Bohr):\n") + step_list = step.tolist() + + fh.write("-----------------------------------------------------------------------\n" + "Center Atomic Step (Bohr)\n" + "Number Number X Y Z\n" + "-----------------------------------------------------------------------\n") + for i in range(len(molecules[0])): + fh.write(" {:>5d} {:>3d} {:>14.9f} {:>14.9f} {:>14.9f}\n".format( + i + 1, molecules[0][i]['na'], + step_list.pop(0), step_list.pop(0), step_list.pop(0))) + + fh.write("-----------------------------------------------------------------------\n") + + step_max = np.amax(np.absolute(step)) + step_rms = np.sqrt(np.mean(np.square(step))) + + fh.write(" Max Step = {:>14.9f} RMS Step = {:>14.9f}\n\n".format( + step_max, step_rms)) + + return step + + + +def read_position(molecule): + + position_list = [] + for atom in molecule: + position_list.extend([ atom['rx'], atom['ry'], atom['rz'] ]) + position = np.array(position_list) + position *= ang2bohr + + return position + + + +def update_molecule(position, fh): + + position_in_ang = (position * bohr2ang).tolist() + new_molecule = deepcopy(molecules[0]) + for atom in new_molecule: + atom['rx'] = position_in_ang.pop(0) + atom['ry'] = position_in_ang.pop(0) + atom['rz'] = position_in_ang.pop(0) + + rmsd, molecules[0] = rmsd_fit(new_molecule, molecules[0]) + + fh.write("\nProjected new conformation of reference molecule with RMSD fit\n") + fh.write("RMSD = {:>8.5f} Angstrom\n".format(rmsd)) + + return + + + +def update_hessian(step, cur_gradient, old_gradient, hessian): ## According to the BFGS + + dif_gradient = cur_gradient - old_gradient + + mat1 = 1/np.dot(dif_gradient, step) * np.matmul(dif_gradient.T, dif_gradient) + mat2 = 1/np.dot(step, np.matmul(hessian, step.T).T) + mat2 *= np.matmul( np.matmul(hessian, step.T), np.matmul(step, hessian) ) + + hessian += mat1 - mat2 + + return hessian + + + +def populate_asec_vdw(cycle, fh): + + asec_charges = [] # (rx, ry, rz, chg) + vdw_meanfield = [] # (rx, ry, rz, eps, sig) + + if dice['nstep'][-1] % dice['isave'] == 0: + nconfigs = round(dice['nstep'][-1] / dice['isave']) + else: + nconfigs = int(dice['nstep'][-1] / dice['isave']) + + norm_factor = nconfigs * player['nprocs'] + + nsitesref = len(molecules[0]) + len(ghost_atoms) + len(lp_atoms) + + nsites_total = dice['nmol'][0] * nsitesref + for i in range(1, len(dice['nmol'])): + nsites_total += dice['nmol'][i] * len(molecules[i]) + + thickness = [] + picked_mols = [] + + for proc in range(1, player['nprocs'] + 1): ## Run over folders + + path = "step{:02d}".format(cycle) + os.sep + "p{:02d}".format(proc) + file = path + os.sep + dice['outname'] + ".xyz" + if not os.path.isfile(file): + sys.exit("Error: cannot find file {}".format(file)) + try: + with open(file) as xyzfh: + xyzfile = xyzfh.readlines() + except: + sys.exit("Error: cannot open file {}".format(file)) + + for config in range(nconfigs): ## Run over configs in a folder + + if int( xyzfile.pop(0).split()[0] ) != nsites_total: + sys.exit("Error: wrong number of sites in file {}".format(file)) + + box = xyzfile.pop(0).split()[-3:] + box = [ float(box[0]), float(box[1]), float(box[2]) ] + sizes = sizes_of_molecule(molecules[0]) + thickness.append( min([ (box[0] - sizes[0])/2, (box[1] - sizes[1])/2, + (box[2] - sizes[2])/2 ]) ) + + xyzfile = xyzfile[nsitesref:] ## Skip the first (reference) molecule + mol_count = 0 + for type in range(len(dice['nmol'])): ## Run over types of molecules + + if type == 0: + nmols = dice['nmol'][0] - 1 + else: + nmols = dice['nmol'][type] + + for mol in range(nmols): ## Run over molecules of each type + + new_molecule = [] + for site in range(len(molecules[type])): ## Run over sites of each molecule + + new_molecule.append({}) + line = xyzfile.pop(0).split() + + if line[0].title() != atomsymb[molecules[type][site]['na']].strip(): + sys.exit("Error reading file {}".format(file)) + + new_molecule[site]['na'] = molecules[type][site]['na'] + new_molecule[site]['rx'] = float(line[1]) + new_molecule[site]['ry'] = float(line[2]) + new_molecule[site]['rz'] = float(line[3]) + new_molecule[site]['chg'] = molecules[type][site]['chg'] + new_molecule[site]['eps'] = molecules[type][site]['eps'] + new_molecule[site]['sig'] = molecules[type][site]['sig'] + + dist = minimum_distance(molecules[0], new_molecule) + if dist < thickness[-1]: + mol_count += 1 + for atom in new_molecule: + asec_charges.append({}) + vdw_meanfield.append({}) + + asec_charges[-1]['rx'] = atom['rx'] + asec_charges[-1]['ry'] = atom['ry'] + asec_charges[-1]['rz'] = atom['rz'] + asec_charges[-1]['chg'] = atom['chg'] / norm_factor + + if player['vdwforces'] == "yes": + vdw_meanfield[-1]['rx'] = atom['rx'] + vdw_meanfield[-1]['ry'] = atom['ry'] + vdw_meanfield[-1]['rz'] = atom['rz'] + vdw_meanfield[-1]['eps'] = atom['eps'] + vdw_meanfield[-1]['sig'] = atom['sig'] + + #### Read lines with ghosts or lps in molecules of type 0 (reference) + #### and, if dist < thickness, appends to asec + if type == 0: + for ghost in ghost_atoms: + line = xyzfile.pop(0).split() + if line[0] != dice_ghost_label: + sys.exit("Error reading file {}".format(file)) + if dist < thickness[-1]: + asec_charges.append({}) + asec_charges[-1]['rx'] = float(line[1]) + asec_charges[-1]['ry'] = float(line[2]) + asec_charges[-1]['rz'] = float(line[3]) + asec_charges[-1]['chg'] = ghost['chg'] / norm_factor + + for lp in lp_atoms: + line = xyzfile.pop(0).split() + if line[0] != dice_ghost_label: + sys.exit("Error reading file {}".format(file)) + if dist < thickness[-1]: + asec_charges.append({}) + asec_charges[-1]['rx'] = float(line[1]) + asec_charges[-1]['ry'] = float(line[2]) + asec_charges[-1]['rz'] = float(line[3]) + asec_charges[-1]['chg'] = lp['chg'] / norm_factor + + picked_mols.append(mol_count) + + fh.write("Done\n") + + string = "In average, {:^7.2f} molecules ".format(sum(picked_mols)/norm_factor) + string += "were selected from each of the {} configurations ".format(len(picked_mols)) + string += "of the production simulations to form the ASEC, comprising a shell with " + string += "minimum thickness of {:>6.2f} Angstrom\n".format(sum(thickness)/norm_factor) + + fh.write(textwrap.fill(string, 86)) + fh.write("\n") + + otherfh = open("ASEC.dat", "w") + for charge in asec_charges: + otherfh.write("{:>10.5f} {:>10.5f} {:>10.5f} {:>11.8f}\n".format( + charge['rx'], charge['ry'], charge['rz'], charge['chg'])) + otherfh.close() + + return asec_charges + + + +def principal_axes(inertia_tensor): + + try: + evals, evecs = linalg.eigh(inertia_tensor) + except: + sys.exit("Error: diagonalization of inertia tensor did not converge") + + return evals, evecs + + + +def print_geom(cycle, fh): + + fh.write("{}\n".format(len(molecules[0]))) + fh.write("Cycle # {}\n".format(cycle)) + for atom in molecules[0]: + symbol = atomsymb[atom['na']] + fh.write("{:<2s} {:>10.6f} {:>10.6f} {:>10.6f}\n".format(symbol, + atom['rx'], atom['ry'], atom['rz'])) + + return + + + +def print_mol_info(molecule, fh): + + com = center_of_mass(molecule) + fh.write(" Center of mass = ( {:>10.4f} , {:>10.4f} , {:>10.4f} )\n".format(com[0], + com[1], com[2])) + inertia = inertia_tensor(molecule) + evals, evecs = principal_axes(inertia) + + fh.write(" Moments of inertia = {:>9E} {:>9E} {:>9E}\n".format(evals[0], + evals[1], evals[2])) + + fh.write(" Major principal axis = ( {:>10.6f} , {:>10.6f} , {:>10.6f} )\n".format( + evecs[0,0], evecs[1,0], evecs[2,0])) + fh.write(" Inter principal axis = ( {:>10.6f} , {:>10.6f} , {:>10.6f} )\n".format( + evecs[0,1], evecs[1,1], evecs[2,1])) + fh.write(" Minor principal axis = ( {:>10.6f} , {:>10.6f} , {:>10.6f} )\n".format( + evecs[0,2], evecs[1,2], evecs[2,2])) + + sizes = sizes_of_molecule(molecule) + fh.write(" Characteristic lengths = ( {:>6.2f} , {:>6.2f} , {:>6.2f} )\n".format( + sizes[0], sizes[1], sizes[2])) + mol_mass = total_mass(molecule) + fh.write(" Total mass = {:>8.2f} au\n".format(mol_mass)) + + chg_dip = charges_and_dipole(molecule) + fh.write(" Total charge = {:>8.4f} e\n".format(chg_dip[0])) + fh.write(" Dipole moment = ( {:>9.4f} , {:>9.4f} , {:>9.4f} ) Total = {:>9.4f} Debye\n\n".format( + chg_dip[1], chg_dip[2], chg_dip[3], chg_dip[4])) + + return + + + +def sizes_of_molecule(molecule): + + x_list = [] + y_list = [] + z_list = [] + for atom in molecule: + if atom['na'] != ghost_number: + x_list.append(atom['rx']) + y_list.append(atom['ry']) + z_list.append(atom['rz']) + + x_max = max(x_list) + x_min = min(x_list) + y_max = max(y_list) + y_min = min(y_list) + z_max = max(z_list) + z_min = min(z_list) + + sizes = [x_max - x_min, y_max - y_min, z_max - z_min] + + return sizes + + + +def standard_orientation(molecule): + + center_of_mass_to_origin(molecule) + tensor = inertia_tensor(molecule) + evals, evecs = principal_axes(tensor) + if round(linalg.det(evecs)) == -1: + evecs[0,2] *= -1 + evecs[1,2] *= -1 + evecs[2,2] *= -1 + if round(linalg.det(evecs)) != 1: + sys.exit("Error: could not make a rotation matrix while adopting the standard orientation") + + rot_matrix = evecs.T + for atom in molecule: + position = np.array([ atom['rx'], atom['ry'], atom['rz'] ]) + new_position = np.matmul(rot_matrix, position.T).T + atom['rx'] = new_position[0] + atom['ry'] = new_position[1] + atom['rz'] = new_position[2] + + return + + + +def total_mass(molecule): + + mass = 0 + for atom in molecule: + mass += atom['mass'] + + return mass + + + +def translate(molecule, vector): + + new_molecule = deepcopy(molecule) + for atom in new_molecule: + atom['rx'] += vector[0] + atom['ry'] += vector[1] + atom['rz'] += vector[2] + + return new_molecule + + + +def rmsd_fit(projecting_mol, reference_mol): + + if len(projecting_mol) != len(reference_mol): + sys.exit("Error in RMSD fit procedure: molecules have different number of atoms") + dim = len(projecting_mol) + + new_projecting_mol = deepcopy(projecting_mol) + new_reference_mol = deepcopy(reference_mol) + + center_of_mass_to_origin(new_projecting_mol) + center_of_mass_to_origin(new_reference_mol) + + x = [] + y = [] + + for atom in new_projecting_mol: + x.extend([ atom['rx'], atom['ry'], atom['rz'] ]) + + for atom in new_reference_mol: + y.extend([ atom['rx'], atom['ry'], atom['rz'] ]) + + x = np.array(x).reshape(dim, 3) + y = np.array(y).reshape(dim, 3) + + r = np.matmul(y.T, x) + rr = np.matmul(r.T, r) + + try: + evals, evecs = linalg.eigh(rr) + except: + sys.exit("Error: diagonalization of RR matrix did not converge") + + a1 = evecs[:,2].T + a2 = evecs[:,1].T + a3 = np.cross(a1, a2) + + A = np.array([ a1[0], a1[1], a1[2], a2[0], a2[1], a2[2], a3[0], a3[1], a3[2] ]) + A = A.reshape(3,3) + + b1 = np.matmul(r, a1.T).T # or np.dot(r, a1) + b1 /= linalg.norm(b1) + b2 = np.matmul(r, a2.T).T # or np.dot(r, a2) + b2 /= linalg.norm(b2) + b3 = np.cross(b1, b2) + + B = np.array([ b1[0], b1[1], b1[2], b2[0], b2[1], b2[2], b3[0], b3[1], b3[2] ]) + B = B.reshape(3,3).T + + rot_matrix = np.matmul(B, A) + x = np.matmul(rot_matrix, x.T).T + + rmsd = 0 + for i in range(dim): + rmsd += (x[i,0] - y[i,0])**2 + (x[i,1] - y[i,1])**2 + (x[i,2] - y[i,2])**2 + rmsd = math.sqrt(rmsd/dim) + + for i in range(dim): + new_projecting_mol[i]['rx'] = x[i,0] + new_projecting_mol[i]['ry'] = x[i,1] + new_projecting_mol[i]['rz'] = x[i,2] + + tr_vector = center_of_mass(reference_mol) + projected_mol = translate(new_projecting_mol, tr_vector) + + return rmsd, projected_mol + + + diff --git a/DPpack/Molcas.py b/DPpack/Molcas.py new file mode 100644 index 0000000..4d8a39a --- /dev/null +++ b/DPpack/Molcas.py @@ -0,0 +1,348 @@ +import os, sys +import textwrap +import subprocess + +from DPpack.PTable import * +from DPpack.SetGlobals import * +from DPpack.MolHandling import * +from DPpack.Misc import * + +####################################### functions ###################################### + +def read_forces_log(file, fh): + + forces = [] + try: + with open(file) as tmpfh: + logfile = tmpfh.readlines() + except: + sys.exit("Error: cannot open file {}".format(file)) + + start = logfile.pop(0).strip() + while start.find("Molecular gradients") < 0: ## expression not found + start = logfile.pop(0).strip() + + logfile = logfile[7:] ## skip next 7 lines + + for i in range(len(molecules[0])): + values = logfile.pop(0).split() + values = values[1:] + forces.extend([ float(x) for x in values ]) + + gradient = np.array(forces) + + fh.write("\nGradient read from file {}:\n".format(file)) + fh.write("-----------------------------------------------------------------------\n" + "Center Atomic Forces (Hartree/Bohr)\n" + "Number Number X Y Z\n" + "-----------------------------------------------------------------------\n") + for i in range(len(molecules[0])): + fh.write(" {:>5d} {:>3d} {:>14.9f} {:>14.9f} {:>14.9f}\n".format( + i + 1, molecules[0][i]['na'], forces.pop(0), forces.pop(0), forces.pop(0))) + + fh.write("-----------------------------------------------------------------------\n") + + force_max = np.amax(np.absolute(gradient)) + force_rms = np.sqrt(np.mean(np.square(gradient))) + + fh.write(" Max Force = {:>14.9f} RMS Force = {:>14.9f}\n\n".format( + force_max, force_rms)) + + return gradient + + + +def read_hessian_log(file): + + force_const = [] + try: + with open(file) as tmpfh: + logfile = tmpfh.readlines() + except: + sys.exit("Error: cannot open file {}".format(file)) + + start = logfile.pop(0).strip() + while start.find("Force constant matrix") < 0: + start = logfile.pop(0).strip() + + logfile = logfile[1:] ## skip next 1 line + + degrees = 3 * len(molecules[0]) + dim = degrees + last = round(dim * dim) + count = 0 + while True: + values = logfile.pop(0).rstrip() + while len(values) != 0: + new_value = values[:16] + values = values[16:] + force_const.append(float(new_value)) + count += 1 + + if count >= last: + break + + hessian = np.array(force_const).reshape(dim, dim) + hessian = hessian[:degrees, :degrees] ## remove degrees related to ghost atoms + + for i in range(degrees): + for j in range(i + 1): + hessian[j,i] = hessian[i,j] ## force the hessian to be symmetric + + return hessian + + + +def print_grad_hessian(cycle, cur_gradient, hessian): + + try: + fh = open("grad_hessian.dat", "w") + except: + sys.exit("Error: cannot open file grad_hessian.dat") + + fh.write("Optimization cycle: {}\n".format(cycle)) + fh.write("Cartesian Gradient\n") + degrees = 3 * len(molecules[0]) + for i in range(degrees): + fh.write(" {:>11.8g}".format(cur_gradient[i])) + if (i + 1) % 5 == 0 or i == degrees - 1: + fh.write("\n") + + fh.write("Cartesian Force Constants\n") + last = degrees * (degrees + 1) / 2 + count = 0 + for i in range(degrees): + for j in range(i + 1): + count += 1 + fh.write(" {:>11.8g}".format(hessian[i,j])) + if count % 5 == 0 or count == last: + fh.write("\n") + + fh.close() + + return + + + +def make_asec_file(cycle, asec_charges): + + path = "step{:02d}".format(cycle) + os.sep + "qm" + file = path + os.sep + "asec.xfield" + try: + fh = open(file, "w") + except: + sys.exit("Error: cannot open file {}".format(file)) + + fh.write("{} Angstrom\n".format(len(asec_charges))) + + ## Write the ASEC: + for charge in asec_charges: + fh.write("{:>10.5f} {:>10.5f} {:>10.5f} {:>11.8f} 0.0 0.0 0.0\n".format( + charge['rx'], charge['ry'], charge['rz'], charge['chg'])) + + fh.write("End of input\n") + fh.close() + + return + + + +def make_force_input(cycle, asec_charges): + + path = "step{:02d}".format(cycle) + os.sep + "qm" + file = path + os.sep + "asec.input" + try: + fh = open(file, "w") + except: + sys.exit("Error: cannot open file {}".format(file)) + + fh.write(" &Gateway\n") + fh.write(" Coord\n") + + nsites = len(molecules[0]) + if cycle >= player['switchcyc']: + nsites += len(ghost_atoms) + len(lp_atoms) + + fh.write("{}\n".format(nsites)) + fh.write("\nForce calculation - Cycle number {}\n".format(cycle)) + + for atom in molecules[0]: + symbol = atomsymb[atom['na']] + fh.write("{:<2s} {:>10.5f} {:>10.5f} {:>10.5f}\n".format(symbol, + atom['rx'], atom['ry'], atom['rz'])) + + ## If also performing charge fit in the same calculation + if cycle >= player['switchcyc']: + for ghost in ghost_atoms: + fh.write("Bq {:>10.5f} {:>10.5f} {:>10.5f}\n".format( + ghost['rx'], ghost['ry'], ghost['rz'])) + + for lp in lp_atoms: + fh.write("Bq {:>10.5f} {:>10.5f} {:>10.5f}\n".format( + lp['rx'], lp['ry'], lp['rz'])) + + fh.write("basis = {}\n".format(molcas['basis'])) + fh.write("group= nosym\n") + fh.write(" XFIELD\n") + fh.write(">>> Include asec.xfield\n") + + if not os.path.isfile(molcas['mbottom']): + sys.exit("Error: cannot find file {} in main directory".format(molcas['mbottom'])) + try: + with open(molcas['mbottom']) as mbottomfile: + mbottom = mbottomfile.readlines() + except: + sys.exit("Error: cannot open file {}".format(molcas['mbottom'])) + + for line in mbottom: + fh.write(line) + + fh.write(" &Alaska\nPNEW\n &SLAPAF\nCartesian\n") + fh.close() + + return + + + +def make_charge_input(cycle, asec_charges): + + path = "step{:02d}".format(cycle) + os.sep + "qm" + file = path + os.sep + "asec.input" + try: + fh = open(file, "w") + except: + sys.exit("Error: cannot open file {}".format(file)) + + fh.write(" &Gateway\n") + fh.write(" Coord\n") + + nsites = len(molecules[0]) + if cycle >= player['switchcyc']: + nsites += len(ghost_atoms) + len(lp_atoms) + + fh.write("{}\n".format(nsites)) + fh.write("\nForce calculation - Cycle number {}\n".format(cycle)) + + for atom in molecules[0]: + symbol = atomsymb[atom['na']] + fh.write("{:<2s} {:>10.5f} {:>10.5f} {:>10.5f}\n".format(symbol, + atom['rx'], atom['ry'], atom['rz'])) + + for ghost in ghost_atoms: + fh.write("Bq {:>10.5f} {:>10.5f} {:>10.5f}\n".format( + ghost['rx'], ghost['ry'], ghost['rz'])) + + for lp in lp_atoms: + fh.write("Bq {:>10.5f} {:>10.5f} {:>10.5f}\n".format( + lp['rx'], lp['ry'], lp['rz'])) + + fh.write("basis = {}\n".format(molcas['basis'])) + fh.write("group= nosym\n") + fh.write(" XFIELD\n") + fh.write(">>> Include asec.xfield\n") + + if not os.path.isfile(molcas['mbottom']): + sys.exit("Error: cannot find file {} in main directory".format(molcas['mbottom'])) + try: + with open(molcas['mbottom']) as mbottomfile: + mbottom = mbottomfile.readlines() + except: + sys.exit("Error: cannot open file {}".format(molcas['mbottom'])) + + for line in mbottom: + fh.write(line) + + fh.close() + + return + + + +def read_charges(file, fh): + + try: + with open(file) as tmpfh: + glogfile = tmpfh.readlines() + except: + sys.exit("Error: cannot open file {}".format(file)) + + start = glogfile.pop(0).strip() + while start != "Fitting point charges to electrostatic potential": + start = glogfile.pop(0).strip() + + glogfile = glogfile[3:] ## Consume 3 more lines + + fh.write("\nAtomic charges:\n") + fh.write("------------------------------------\n") + for atom in molecules[0]: + line = glogfile.pop(0).split() + atom_str = line[1] + charge = float(line[2]) + atom['chg'] = charge + fh.write(" {:<2s} {:>10.6f}\n".format(atom_str, charge)) + + if gaussian['pop'] == "chelpg": + for ghost in ghost_atoms: + line = glogfile.pop(0).split() + atom_str = line[1] + charge = float(line[2]) + ghost['chg'] = charge + fh.write(" {:<2s} {:>10.6f}\n".format(atom_str, charge)) + + for lp in lp_atoms: + line = glogfile.pop(0).split() + atom_str = line[1] + charge = float(line[2]) + lp['chg'] = charge + fh.write(" {:<2s} {:>10.6f}\n".format(atom_str, charge)) + + fh.write("------------------------------------\n") + + return + + + +def run_gaussian(cycle, type, fh): + + path = "step{:02d}".format(cycle) + os.sep + "qm" + work_dir = os.getcwd() + os.chdir(path) + + if type == "force": + infile = "asec.gjf" + elif type == "charge": + infile = "asec2.gjf" + + fh.write("\nCalculation of {}s initiated with Gaussian on {}\n".format(type, date_time())) + + exit_status = subprocess.call([player['qmprog'], infile]) + + if exit_status != 0: + sys.exit("Gaussian process did not exit properly") + + fh.write("Calculation of {}s finished on {}\n".format(type, date_time())) + + os.chdir(work_dir) + + return + + + +def run_formchk(cycle, fh): + + path = "step{:02d}".format(cycle) + os.sep + "qm" + work_dir = os.getcwd() + os.chdir(path) + + fh.write("Formatting the checkpoint file... ") + + exit_status = subprocess.call(["formchk", "asec.chk"]) + + fh.write("Done\n") + + os.chdir(work_dir) + + return + + + diff --git a/DPpack/Optimization.py b/DPpack/Optimization.py new file mode 100644 index 0000000..26c0de4 --- /dev/null +++ b/DPpack/Optimization.py @@ -0,0 +1,266 @@ +import sys, math +from copy import deepcopy + +import numpy as np +from numpy import linalg + +from DPpack.SetGlobals import * + + +epsilon = 1e-8 + +####################################### functions ###################################### + +def best_previous_point(): + + min_energy = 0 + idx = 0 + for energy in internal['energy'][:-1]: + if energy < min_energy or abs(energy - min_energy) < 1e-10: + min_energy = energy + min_idx = idx + idx += 1 + + return min_idx + + + +def best_point(): + + min_energy = 0 + idx = 0 + for energy in internal['energy']: + if energy < min_energy or abs(energy - min_energy) < 1e-10: + min_energy = energy + min_idx = idx + idx += 1 + + return min_idx + + + +def line_search(fh): + + X1 = internal['position'][-1] # numpy array + e1 = internal['energy'][-1] + G1 = internal['gradient'][-1] # numpy array + + idx = best_previous_point() + X0 = internal['position'][idx] # numpy array + e0 = internal['energy'][idx] + G0 = internal['gradient'][idx] # numpy array + + # First try a quartic fit + fh.write("Attempting a quartic fit.\n") + success, y0 = quartic_fit(X0, X1, e0, e1, G0, G1, fh) + if success and y0 > 0: + if y0 < 1: + new_point = X0 + y0*(X1 - X0) + new_gradient = interpolate_gradient(G0, G1, y0) + new_gradient = perpendicular_projection(new_gradient, X1 - X0) + fh.write("Line search succeded.\n") + return True, new_point, new_gradient + else: + idx = best_point() + if idx == len(internal['energy']) - 1: + new_point = X0 + y0*(X1 - X0) + new_gradient = interpolate_gradient(G0, G1, y0) + new_gradient = perpendicular_projection(new_gradient, X1 - X0) + fh.write("Line search succeded.\n") + return True, new_point, new_gradient + else: + fh.write("Quartic step is not acceptable. ") + elif success: + fh.write("Quartic step is not acceptable. ") + + # If no condition is met, then y0 is unacceptable. Try the cubic fit next + fh.write("Attempting a cubic fit.\n") + success, y0 = cubic_fit(X0, X1, e0, e1, G0, G1, fh) + if success and y0 > 0: + if y0 < 1: + new_point = X0 + y0*(X1 - X0) + new_gradient = interpolate_gradient(G0, G1, y0) + new_gradient = perpendicular_projection(new_gradient, X1 - X0) + fh.write("Line search succeded.\n") + return True, new_point, new_gradient + else: + previous_step = X1 - internal['position'][-2] + previous_step_size = linalg.norm(previous_step) + new_point = X0 + y0*(X1 - X0) + step = new_point - X1 + step_size = linalg.norm(step) + if step_size < previous_step_size: + new_gradient = interpolate_gradient(G0, G1, y0) + new_gradient = perpendicular_projection(new_gradient, X1 - X0) + fh.write("Line search succeded.\n") + return True, new_point, new_gradient + else: + fh.write("Cubic step is not acceptable. ") + elif success: + fh.write("Cubic step is not acceptable. ") + + # If no condition is met again, then all fits fail. + fh.write("All fits fail. ") + + # Then, if the latest point is not the best, use y0 = 0.5 (step to the midpoint) + idx = best_point() + if idx < len(internal['energy']) - 1: + y0 = 0.5 + new_point = X0 + y0*(X1 - X0) + new_gradient = interpolate_gradient(G0, G1, y0) + new_gradient = perpendicular_projection(new_gradient, X1 - X0) + fh.write("Moving to the midpoint.\n") + return True, new_point, new_gradient + + # If the latest point is the best point, no linear search is done + fh.write("No linear search will be used in this step.\n") + + return False, None, None + + + +## For cubic and quartic fits, G0 and G1 are the gradient vectors + +def cubic_fit(X0, X1, e0, e1, G0, G1, fh): + + line = X1 - X0 + line /= linalg.norm(line) + + g0 = np.dot(G0, line) + g1 = np.dot(G1, line) + + De = e1 - e0 + + fh.write("De = {:<18.15e} g0 = {:<12.8f} g1 = {:<12.8f}\n".format(De, g0, g1)) + + alpha = g1 + g0 - 2*De + if abs(alpha) < epsilon: + fh.write("Cubic fit failed: alpha too small\n") + return False, None + + beta = 3*De - 2*g0 - g1 + discriminant = 4 * (beta**2 - 3*alpha*g0) + if discriminant < 0: + fh.write("Cubic fit failed: no minimum found (negative Delta)\n") + return False, None + if abs(discriminant) < epsilon: + fh.write("Cubic fit failed: no minimum found (null Delta)\n") + return False, None + + y0 = (-beta + math.sqrt(discriminant/4)) / (3*alpha) + fh.write("Minimum found with y0 = {:<8.4f}\n".format(y0)) + + return True, y0 + + + +def quartic_fit(X0, X1, e0, e1, G0, G1, fh): + + line = X1 - X0 + line /= linalg.norm(line) + + g0 = np.dot(G0, line) + g1 = np.dot(G1, line) + + De = e1 - e0 + Dg = g1 - g0 + + fh.write("De = {:<18.15e} g0 = {:<12.8f} g1 = {:<12.8f}\n".format(De, g0, g1)) + + if Dg < 0 or De - g0 < 0: + fh.write("Quartic fit failed: negative alpha\n") + return False, None + if abs(Dg) < epsilon or abs(De - g0) < epsilon: + fh.write("Quartic fit failed: alpha too small\n") + return False, None + + discriminant = 16 * (Dg**2 - 3*(g1 + g0 - 2*De)**2) + if discriminant < 0: + fh.write("Quartic fit failed: no minimum found (negative Delta)\n") + return False, None + + alpha1 = (Dg + math.sqrt(discriminant/16)) / 2 + alpha2 = (Dg - math.sqrt(discriminant/16)) / 2 + + fh.write("alpha1 = {:<7.4e} alpha2 = {:<7.4e}\n".format(alpha1, alpha2)) + + alpha = alpha1 + beta = g1 + g0 - 2*De - 2*alpha + gamma = De - g0 - alpha - beta + + y0 = (-1/(2*alpha)) * ((beta**3 - 4*alpha*beta*gamma + 8*g0*alpha**2)/4)**(1/3) + fh.write("Minimum found with y0 = {:<8.4f}\n".format(y0)) + + return True, y0 + + + +def rfo_step(gradient, hessian, type): + + dim = len(gradient) + + aug_hessian = [] + for i in range(dim): + aug_hessian.extend(hessian[i,:].tolist()) + aug_hessian.append(gradient[i]) + + aug_hessian.extend(gradient.tolist()) + aug_hessian.append(0) + + aug_hessian = np.array(aug_hessian).reshape(dim + 1, dim + 1) + + evals, evecs = linalg.eigh(aug_hessian) + + if type == "min": + step = np.array(evecs[:-1,0]) + elif type == "ts": + step = np.array(evecs[:-1,1]) + + return step + + + +def update_trust_radius(): + + if internal['trust_radius'] == None: + internal['trust_radius'] = player['maxstep'] + elif len(internal['energy']) > 1: + X1 = internal['position'][-1] + X0 = internal['position'][-2] + Dx = X1 - X0 + displace = linalg.norm(Dx) + e1 = internal['energy'][-1] + e0 = internal['energy'][-2] + De = e1 - e0 + g0 = internal['gradient'][-2] + h0 = internal['hessian'][-2] + + rho = De / (np.dot(g0, Dx) + 0.5*np.dot(Dx, np.matmul(h0, Dx.T).T)) + + if rho > 0.75 and displace > 0.8*internal['trust_radius']: + internal['trust_radius'] = 2*internal['trust_radius'] + elif rho < 0.25: + internal['trust_radius'] = 0.25*displace + + return + + + +def interpolate_gradient(G0, G1, y0): + + DG = G1 - G0 + gradient = G0 + y0*DG + + return gradient + + + +def perpendicular_projection(vector, line): + + direction = line / linalg.norm(line) + projection = np.dot(vector, direction) * direction + + return vector - projection + + + diff --git a/DPpack/PTable.py b/DPpack/PTable.py new file mode 100644 index 0000000..fe6762d --- /dev/null +++ b/DPpack/PTable.py @@ -0,0 +1,35 @@ +#### Label used in Dice for a ghost atom +dice_ghost_label = "Xx" + +#### Tuple of atom symbols +atomsymb = ( "00", + +"H ", "He", +"Li","Be", "B ","C ","N ","O ","F ","Ne", +"Na","Mg", "Al","Si","P ","S ","Cl","Ar", +"K ","Ca","Sc","Ti","V ","Cr","Mn","Fe","Co","Ni","Cu","Zn","Ga","Ge","As","Se","Br","Kr", +"Rb","Sr","Y ","Zr","Nb","Mo","Tc","Ru","Rh","Pd","Ag","Cd","In","Sn","Sb","Te","I ","Xe", +"Cs","Ba", + "La","Ce","Pr","Nd","Pm","Sm","Eu","Gd","Tb","Dy","Ho","Er","Tm","Yb","Lu", + "Hf","Ta","W ","Re","Os","Ir","Pt","Au","Hg","Ti","Pb","Bi","Po","At","Rn", +"Fr","Ra", + "Ac","Th","Pa","U ","Np","Pu","Am","Cm","Bk","Cf","Es","Fm","Md","No","Lr", + dice_ghost_label ) + +#### Tuple of atom masses +atommass = ( 0.0, + +1.0079, 4.0026, +6.9410,9.0122, 10.811,12.011,14.007,15.999,18.998,20.180, +22.990,24.305, 26.982,28.086,30.974,32.065,35.453,39.948, +39.098,40.078,44.956,47.867,50.942,51.996,54.938,55.845,58.933,58.693,63.546,65.409,69.723,72.640,74.922,78.960,79.904,83.798, +85.468,87.620,88.906,91.224,92.906,95.940,98.000,101.07,102.91,106.42,107.87,112.41,114.82,118.71,121.76,127.60,126.90,131.29, +132.91,137.33, + 138.91,140.12,140.91,144.24,145.00,150.36,151.96,157.25,158.93,162.50,164.93,167.26,168.93,173.04,174.97, + 178.49,180.95,183.84,186.21,190.23,192.22,195.08,196.97,200.59,204.38,207.20,208.98,209.00,210.00,222.00, +223.00,226.00, + 227.00,232.04,231.04,238.03,237.00,244.00,243.00,247.00,247.00,251.00,252.00,257.00,258.00,259.00,262.00, + 0.000 ) + +#### Number of the ghost atom +ghost_number = len(atomsymb) - 1 \ No newline at end of file diff --git a/DPpack/SetGlobals.py b/DPpack/SetGlobals.py new file mode 100644 index 0000000..61fd7dd --- /dev/null +++ b/DPpack/SetGlobals.py @@ -0,0 +1,813 @@ +import os, sys +import shutil +import textwrap + +from DPpack.PTable import * +from DPpack.Misc import * + +#### Global hashes that control the behaviour of Diceplayer + +player = {} +dice = {} +gaussian = {} +molcas = {} +internal = {} + +####################################################################### +#### Global parameters that MAY be given by the user #### +#### (If not given by the user, default values will be used) #### +####################################################################### + +## Diceplayer: +player['maxcyc'] = 1 +player['initcyc'] = 1 # May restart an optimization (append to geoms.xyz from start) +player['nprocs'] = 1f +player['switchcyc'] = 3 # At which step start doing only one QM calculation (geom & chg) +player['altsteps'] = 20000 # Steps for thermalization when starting from previous step +player['maxstep'] = 0.3 # Maxstep for geometry relaxation in Bohr +player['qmprog'] = "g09" +player['opt'] = "yes" +player['freq'] = "no" +player['readhessian'] = "no" +player['lps'] = "no" +player['ghosts'] = "no" +player['vdwforces'] = "no" +player['tol_factor'] = 1.2 # Factor to multiply the default tolerance values + +## Dice: +dice['title'] = "Diceplayer run" +dice['progname'] = "dice" +dice['temp'] = 300.0 +dice['press'] = 1.0 +dice['isave'] = 1000 # ASEC construction will take this into account +dice['ncores'] = 1 + +## Gaussian: +gaussian['mem'] = None +gaussian['keywords'] = None +gaussian['chgmult'] = [0, 1] +gaussian['gmiddle'] = None # In each case, if a filename is given, its content will be +gaussian['gbottom'] = None # inserted in the gaussian input +gaussian['pop'] = "chelpg" +gaussian['chglevel'] = None + +## Molcas: +molcas['orbfile'] = "input.exporb" +molcas['root'] = 1 + + +######################################################################## +#### Global parameters that MUST be given by the user #### +######################################################################## + +## Dice: +dice['dens'] = None # Investigate the possibility of using 'box = Lx Ly Lz' instead. +#dice['box'] = None # So 'geom' would be set by diceplayer and 'cutoff' would be + # switched off. One of them must be given. +dice['ljname'] = None +dice['outname'] = None +dice['nmol'] = [] # Up to 4 integer values related to up to 4 molecule types +dice['nstep'] = [] # 2 or 3 integer values related to 2 or 3 simulations + # (NVT th + NVT eq) or (NVT th + NPT th + NPT eq). + # This will control the 'nstep' keyword of Dice + +## Gaussian: +gaussian['level'] = None + +## Molcas: +molcas['mbottom'] = None +molcas['basis'] = None + + +## The following Dice keywords will be handled automatically by Diceplayer: +## * init ("yes" in the first thermalization and "yesreadxyz" for thermalizations +## starting from a previous step / "no" in subsequent simulations) +## * vstep ("0" for NVT simulations and 'nstep'/5 for NPT simulations) +## * nstep ('nstep' for NVT and "5" for NPT simulations ) +## * irdf ("0" for thermalizations and "10*nprocs" for equilibrium) +## * seed (will be generated randomly each time a Dice input is created) + +## The following Dice keywords will be set constant by Diceplayer for all simulations +## * mstop = 1 (So to guarantee that the ASEC will be correctly built) +## * accum = no (There is never a simulation continuation in Diceplayer) +## * iprint = 1 (Print energy info every step in Dice output) + +## All the other Dice keywords will not be altered from their default values +## and therefore are not mentioned in Diceplayer + + +##################################################################### +#### Global parameters that are not accessible to the user #### +#### (Intended to be used only internally by the program) #### +##################################################################### + +## Diceplayer: +internal['tol_rms_force'] = 3e-4 # Hartree/Bohr +internal['tol_max_force'] = 4.5e-4 # Hartree/Bohr +internal['tol_rms_step'] = 1.2e-3 # Bohr +internal['tol_max_step'] = 1.8e-3 # Bohr +internal['trust_radius'] = None + +## Dice: +internal['combrule'] = None +internal['randominit'] = None + +## Other global variables: +molecules = [] # Armazena todas as informacoes sobre cada tipo de molecula + # (lbl, na, rx, ry, rz, chg, eps, sig, mass) + +internal['ghost_types'] = [] +internal['ghost_atoms'] = [] # Store the ghost atoms (off-atom charge sites) in the QM molecule + # (rx, ry, rz, chg) +internal['lp_types'] = [] +internal['lp_atoms'] = [] # Store the lone pairs (special off-atom charge sites) in the QM molecule + # (rx, ry, rz, chg) + +## Numpy arrays: +step = [] ## Values in Bohr +internal['position'] = [] +internal['energy'] = [] ## Values in Hartree +internal['gradient'] = [] ## Values in Hartree/Bohr +internal['hessian'] = [] ## Values in Hartree/Bohr^2 + +## Conversion factors: +bohr2ang = 0.52917721092 +ang2bohr = 1/bohr2ang + +###################################################################### +#### Environment variables important for executing Diceplayer #### +###################################################################### + +env = ["OMP_STACKSIZE"] + +####################################### functions ###################################### +## Functions to process the input files and store the values in the global variables ## +########################################################################################## + +def read_keywords(infile): + + try: + with open(infile) as fh: + controlfile = fh.readlines() + except EnvironmentError: + sys.exit("Error: cannot open file {}".format(infile)) + + for line in controlfile: + + key, value = line.partition("=")[::2] # Discards the '=' + key = key.strip().lower() + if key in ('title', 'keywords'): + value = value.strip() + else: + value = value.split() + + #### Read the Diceplayer related keywords + if key in player and len(value) != 0: ## 'value' is not empty! + + if key == 'qmprog' and value[0].lower() in ("g03", "g09", "g16", "molcas"): + player[key] = value[0].lower() + + elif key == 'opt' and value[0].lower() in ("yes", "no", "ts"): + player[key] = value[0].lower() + + #elif key == 'zipprog' and value[0].lower() in ("zip", "gzip", "bzip"): + #player[key] = value[0].lower() + + elif key in ('lps', 'ghosts') and value[0].lower() in ("yes", "no"): + player[key] = value[0].lower() + + elif key in ('readhessian', 'vdwforces') and value[0].lower() in ("yes", "no"): + player[key] = value[0].lower() + + elif key in ('maxcyc', 'initcyc', 'nprocs', 'altsteps', 'switchcyc'): + err = "Error: expected a positive integer for keyword {} in file {}".format(key, infile) + try: + new_value = int(value[0]) + if new_value >= 1: + player[key] = new_value + elif key == 'altsteps' and new_value == 0: + player[key] = 0 + except ValueError: + sys.exit(err) + + elif key == 'maxstep': # Cannot be less than 0.01 + err = "Error: expected a float greater than 0.01 for keyword {} in file {}".format(key, infile) + try: + new_value = float(value[0]) + if new_value < 0.01: + sys.exit(err) + else: + player[key] = new_value + except ValueError: + sys.exit(err) + + #### Read the Dice related keywords + elif key in dice and len(value) != 0: ## 'value' is not empty! + + if key == 'title': + dice[key] = value + + elif key in ('ljname', 'outname', 'progname'): + dice[key] = value[0] + + elif key in ('ncores', 'isave'): + err = "Error: expected a positive integer for keyword {} in file {}".format(key, infile) + if not value[0].isdigit(): + sys.exit(err) + new_value = int(value[0]) + if new_value >= 1: + dice[key] = new_value + + elif key in ('temp', 'press', 'dens'): # Cannot be less than 1e-10 + err = "Error: expected a positive float for keyword {} in file {}".format(key, infile) + try: + new_value = float(value[0]) + if new_value < 1e-10: + sys.exit(err) + else: + dice[key] = new_value + except ValueError: + sys.exit(err) + + elif key == 'nmol': # If defined, must be well defined (only positive integer values) + err = "Error: expected 1 to 4 positive integers for keyword {} in file {}".format(key, infile) + args = min(4, len(value)) + for i in range(args): + if value[i].isdigit(): + new_value = int(value[i]) + if new_value < 1: + sys.exit(err) + else: + dice[key].append(new_value) + elif i == 0: + sys.exit(err) + else: + break + + elif key == 'nstep': # If defined, must be well defined (only positive integer values) + err = "Error: expected 2 or 3 positive integers for keyword {} in file {}".format(key, infile) + if len(value) < 2: + sys.exit(err) + args = min(3, len(value)) + for i in range(args): + if value[i].isdigit(): + new_value = int(value[i]) + if new_value < 1: + sys.exit(err) + else: + dice[key].append(new_value) + elif i < 2: + sys.exit(err) + else: + break + + #### Read the Gaussian related keywords + elif key in gaussian and len(value) != 0: ## 'value' is not empty! + + if key == 'mem': # Memory in MB (minimum of 100) + err = "Error: expected a positive integer for keyword {} in file {}".format(key, infile) + if not value[0].isdigit(): + sys.exit(err) + new_value = int(value[0]) + if new_value >= 100: + gaussian[key] = new_value + + elif key == 'keywords': + gaussian[key] = value + + elif key == 'chgmult': # If defined, must be well defined (2 integer values) + err = "Error: expected 2 integers for keyword {} in file {}".format(key, infile) + if len(value) < 2: + sys.exit(err) + for i in range (2): + try: + gaussian[key][i] = int(value[i]) + except ValueError: + sys.exit(err) + + elif key in ('level', 'chglevel'): + gaussian[key] = value[0] + + elif key in ('gmiddle', 'gbottom'): + gaussian[key] = value[0] + + elif key == 'pop' and value[0].lower() in ("chelpg", "mk", "nbo"): + gaussian[key] = value[0].lower() + + #### Read the Molcas related keywords + elif key in molcas and len(value) != 0: ## 'value' is not empty! + + if key == 'root': # If defined, must be well defined (only positive integer values) + err = "Error: expected a positive integer for keyword {} in file {}".format(key, infile) + if not value[0].isdigit(): + sys.exit(err) + new_value = int(value[0]) + if new_value >= 1: + molcas[key] = new_value + + elif key in ('mbottom', 'orbfile'): + molcas[key] = value[0] + + elif key == 'basis': + molcas[key] = value[0] + + #### End + return + + + +def check_keywords(infile): + + min_steps = 20000 + + if dice['ljname'] == None: + sys.exit("Error: 'ljname' keyword not specified in file {}".format(infile)) + + if dice['outname'] == None: + sys.exit("Error: 'outname' keyword not specified in file {}".format(infile)) + + if dice['dens'] == None: + sys.exit("Error: 'dens' keyword not specified in file {}".format(infile)) + + if len(dice['nmol']) == 0: + sys.exit("Error: 'nmol' keyword not defined appropriately in file {}".format(infile)) + + if len(dice['nstep']) == 0: + sys.exit("Error: 'nstep' keyword not defined appropriately in file {}".format(infile)) + + ## Check only if QM program is Gaussian: + if player['qmprog'] in ("g03", "g09", "g16"): + if gaussian['level'] == None: + sys.exit("Error: 'level' keyword not specified in file {}".format(infile)) + + if gaussian['gmiddle'] != None: + if not os.path.isfile(gaussian['gmiddle']): + sys.exit("Error: file {} not found".format(gaussian['gmiddle'])) + + if gaussian['gbottom'] != None: + if not os.path.isfile(gaussian['gbottom']): + sys.exit("Error: file {} not found".format(gaussian['gbottom'])) + + if gaussian['pop'] != "chelpg" and (player['ghosts'] == "yes" or player['lps'] == "yes"): + sys.exit("Error: ghost atoms or lone pairs only available with 'pop = chelpg')") + + if gaussian['chglevel'] == None: + gaussian['chglevel'] = gaussian['level'] + + ## Check only if QM program is Molcas: + if player['qmprog'] == "molcas": + + if molcas['mbottom'] == None: + sys.exit("Error: 'mbottom' keyword not specified in file {}".format(infile)) + else: + if not os.path.isfile(molcas['mbottom']): + sys.exit("Error: file {} not found".format(molcas['mbottom'])) + + if molcas['basis'] == None: + sys.exit("Error: 'basis' keyword not specified in file {}".format(infile)) + + + if player['altsteps'] != 0: + + ### Verifica se tem mais de 1 molecula QM + ### (No futuro usar o RMSD fit para poder substituir todas as moleculas QM + ### no arquivo outname.xy - Need to change the make_init_file!!) + if dice['nmol'][0] > 1: + sys.exit("Error: altsteps > 0 only possible with 1 QM molecule (nmol = 1 n2 n3 n4)") + + # if not zero, altsteps cannot be less than min_steps + player['altsteps'] = max(min_steps, player['altsteps']) + # altsteps value is always the nearest multiple of 1000 + player['altsteps'] = round(player['altsteps'] / 1000) * 1000 + + + for i in range(len(dice['nstep'])): + # nstep can never be less than min_steps + dice['nstep'][i] = max(min_steps, dice['nstep'][i]) + # nstep values are always the nearest multiple of 1000 + dice['nstep'][i] = round(dice['nstep'][i] / 1000) * 1000 + + # isave must be between 100 and 2000 + dice['isave'] = max(100, dice['isave']) + dice['isave'] = min(2000, dice['isave']) + # isave value is always the nearest multiple of 100 + dice['isave'] = round(dice['isave'] / 100) * 100 + + return + + + +def print_keywords(fh): + + fh.write("##########################################################################################\n" + "############# Welcome to DICEPLAYER version 1.0 #############\n" + "##########################################################################################\n" + "\n") + fh.write("Your python version is {}\n".format(sys.version)) + fh.write("\n") + fh.write("Program started on {}\n".format(weekday_date_time())) + fh.write("\n") + fh.write("Environment variables:\n") + for var in env: + fh.write("{} = {}\n".format(var, + (os.environ[var] if var in os.environ else "Not set"))) + + fh.write("\n==========================================================================================\n" + " CONTROL variables being used in this run:\n" + "------------------------------------------------------------------------------------------\n" + "\n") + + for key in sorted(player): + if player[key] != None: + if isinstance(player[key], list): + string = " ".join(str(x) for x in player[key]) + fh.write("{} = {}\n".format(key, string)) + else: + fh.write("{} = {}\n".format(key, player[key])) + + fh.write("\n") + + fh.write("------------------------------------------------------------------------------------------\n" + " DICE variables being used in this run:\n" + "------------------------------------------------------------------------------------------\n" + "\n") + + for key in sorted(dice): + if dice[key] != None: + if isinstance(dice[key], list): + string = " ".join(str(x) for x in dice[key]) + fh.write("{} = {}\n".format(key, string)) + else: + fh.write("{} = {}\n".format(key, dice[key])) + + fh.write("\n") + + if player['qmprog'] in ("g03", "g09", "g16"): + + fh.write("------------------------------------------------------------------------------------------\n" + " GAUSSIAN variables being used in this run:\n" + "------------------------------------------------------------------------------------------\n" + "\n") + + for key in sorted(gaussian): + if gaussian[key] != None: + if isinstance(gaussian[key], list): + string = " ".join(str(x) for x in gaussian[key]) + fh.write("{} = {}\n".format(key, string)) + else: + fh.write("{} = {}\n".format(key, gaussian[key])) + + fh.write("\n") + + elif player['qmprog'] == "molcas": + + fh.write("------------------------------------------------------------------------------------------\n" + " MOLCAS variables being used in this run:\n" + "------------------------------------------------------------------------------------------\n" + "\n") + + for key in sorted(molcas): + if molcas[key] != None: + if isinstance(molcas[key], list): + string = " ".join(str(x) for x in molcas[key]) + fh.write("{} = {}\n".format(key, string)) + else: + fh.write("{} = {}\n".format(key, molcas[key])) + + fh.write("\n") + + return + + + +def read_potential(infile): # Deve ser atualizado para o uso de + + try: + with open(dice['ljname']) as file: + ljfile = file.readlines() + except EnvironmentError as err: + sys.exit(err) + + combrule = ljfile.pop(0).split()[0] + if combrule not in ("*", "+"): + sys.exit("Error: expected a '*' or a '+' sign in 1st line of file {}".format(dice['ljname'])) + dice['combrule'] = combrule + + ntypes = ljfile.pop(0).split()[0] + if not ntypes.isdigit(): + sys.exit("Error: expected an integer in the 2nd line of file {}".format(dice['ljname'])) + ntypes = int(ntypes) + + if ntypes != len(dice['nmol']): + sys.exit("Error: number of molecule types in file {} must match that of 'nmol' keyword in file {}".format( + dice['ljname'], infile)) + + line = 2 + for i in range(ntypes): + line += 1 + nsites = ljfile.pop(0).split()[0] + if not nsites.isdigit(): + sys.exit("Error: expected an integer in line {} of file {}".format(line, dice['ljname'])) + + nsites = int(nsites) + molecules.append([]) + + for j in range(nsites): + line += 1 + new_atom = ljfile.pop(0).split() + + if len(new_atom) < 8: + sys.exit("Error: expected at least 8 fields in line {} of file {}".format(line, dice['ljname'])) + + molecules[i].append({}) + + if not new_atom[0].isdigit(): + sys.exit("Error: expected an integer in field 1, line {} of file {}".format(line, dice['ljname'])) + molecules[i][j]['lbl'] = int(new_atom[0]) + + if not new_atom[1].isdigit(): + sys.exit("Error: expected an integer in field 2, line {} of file {}".format(line, dice['ljname'])) + + atnumber = int(new_atom[1]) + if atnumber == ghost_number and i == 0: # Ghost atom not allowed in the QM molecule + sys.exit("Error: found a ghost atom in line {} of file {}".format(line, dice['ljname'])) + molecules[i][j]['na'] = atnumber + + try: + molecules[i][j]['rx'] = float(new_atom[2]) + except: + sys.exit("Error: expected a float in field 3, line {} of file {}".format(line, dice['ljname'])) + + try: + molecules[i][j]['ry'] = float(new_atom[3]) + except: + sys.exit("Error: expected a float in field 4, line {} of file {}".format(line, dice['ljname'])) + + try: + molecules[i][j]['rz'] = float(new_atom[4]) + except: + sys.exit("Error: expected a float in field 5, line {} of file {}".format(line, dice['ljname'])) + + try: + molecules[i][j]['chg'] = float(new_atom[5]) + except: + sys.exit("Error: expected a float in field 6, line {} of file {}".format(line, dice['ljname'])) + + try: + molecules[i][j]['eps'] = float(new_atom[6]) + except: + sys.exit("Error: expected a float in field 7, line {} of file {}".format(line, dice['ljname'])) + + try: + molecules[i][j]['sig'] = float(new_atom[7]) + except: + sys.exit("Error: expected a float in field 8, line {} of file {}".format(line, dice['ljname'])) + + molecules[i][j]['mass'] = atommass[molecules[i][j]['na']] + + if len(new_atom) > 8: + masskey, mass = new_atom[8].partition("=")[::2] + if masskey.lower() == 'mass' and len(mass) !=0: + try: + new_mass = float(mass) + if new_mass > 0: + molecules[i][j]['mass'] = new_mass + except: + sys.exit( + "Error: expected a positive float after 'mass=' in field 9, line {} of file {}".format( + line, dice['ljname'])) + + return + + + +def read_ghosts(): + + max_atom_number = len(molecules[0]) + + try: + with open("ghosts.in") as fh: + ghostfile = fh.readlines() + except EnvironmentError: + sys.exit("Error: cannot open file ghosts.in") + + for line in ghostfile: + + if len(line.split()) > 1: # Discard lines with less than 2 fields + + key, *atom_numbers = line.split() + key = key.lower() + + if key in ("g", "m", "z"): # Discard lines that do not start with g|m|z + ghost_types.append({}) + ghost_types[-1]['type'] = key + ghost_types[-1]['numbers'] = [] + + for num in atom_numbers: + if not num.isdigit(): + sys.exit("Error: in file ghosts.in: only positive integers allowed after letter g|m|z") + new_num = int(num) + if new_num > max_atom_number: + sys.exit("Error: in file ghosts.in: there is no atom number {}".format(new_num)) + else: + ghost_types[-1]['numbers'].append(new_num) + + if len(ghost_types[-1]['numbers']) < 2: + sys.exit("Error: in file ghosts.in: at least 2 atoms are necessary to make a ghost") + + if len(ghost_types) == 0: + sys.exit("Error: no ghost atom found in ghosts.in") + + return + + + +def read_lps(): + + lp_alpha = 104.0 # Default values + lp_dist = 0.7 # + max_lp_type = 2 + min_alpha = 90.0 + max_alpha = 150.0 + min_dist = 0.5 + max_dist = 1.5 + max_atom_number = len(molecules[0]) + + try: + with open("lps.in") as fh: + lpfile = fh.readlines() + except EnvironmentError: + sys.exit("Error: cannot open file lps.in") + + for line in lpfile: + + if len(line.split()) > 1: # Discard lines with less than 2 fields + + type, *atom_numbers = line.split() + + if type.isdigit(): # Discard lines that do not start with an integer + new_type = int(type) + if new_type > max_lp_type: + sys.exit("Error: in file lps.in: allowed LP types from 1 to {}".format(max_lp_type)) + lp_types.append({}) + lp_types[-1]['type'] = new_type + lp_types[-1]['numbers'] = [] + + # Read types 1 and 2 + if new_type in (1, 2): + + if len(atom_numbers) < 3: + sys.exit("Error: in file lps.in: at least 3 atoms are necessary to make LPs type 1 and 2") + for i in range(3): + num = atom_numbers.pop(0) + if not num.isdigit(): + sys.exit("Error: in file lps.in: expected 3 atom numbers after LPs type 1 and 2") + new_num = int(num) + if new_num > max_atom_number or new_num < 1: + sys.exit("Error: in file lps.in: there is no atom number {}".format(new_num)) + else: + lp_types[-1]['numbers'].append(new_num) + + lp_types[-1]['alpha'] = lp_alpha + lp_types[-1]['dist'] = lp_dist + + if len(atom_numbers) != 0: + try: + alpha = float(atom_numbers.pop(0)) + if alpha > min_alpha and alpha < max_alpha: + lp_types[-1]['alpha'] = alpha + else: + atom_numbers = [] + except: + atom_numbers = [] + + if len(atom_numbers) != 0: + try: + dist = float(atom_numbers.pop(0)) + if dist > min_dist and dist < max_dist: + lp_types[-1]['dist'] = dist + except: + None + # End of types 1 and 2 + + if len(lp_types) == 0: + sys.exit("Error: no lone pair found in lps.in") + + return + + + +def print_potential(fh): + + formatstr = "{:<3d} {:>3d} {:>10.5f} {:>10.5f} {:>10.5f} {:>10.6f} {:>9.5f} {:>7.4f} {:>9.4f}\n" + fh.write("\n" + "==========================================================================================\n") + fh.write(" Potential parameters from file {}:\n".format(dice['ljname'])) + fh.write("------------------------------------------------------------------------------------------\n" + "\n") + + fh.write("Combination rule: {}\n".format(dice['combrule'])) + fh.write("Types of molecules: {}\n\n".format(len(molecules))) + + i = 0 + for mol in molecules: + i += 1 + fh.write("{} atoms in molecule type {}:\n".format(len(mol), i)) + fh.write("---------------------------------------------------------------------------------\n" + "Lbl AN X Y Z Charge Epsilon Sigma Mass\n") + fh.write("---------------------------------------------------------------------------------\n") + + for atom in mol: + fh.write(formatstr.format(atom['lbl'], atom['na'], atom['rx'], atom['ry'], atom['rz'], + atom['chg'], atom['eps'], atom['sig'], atom['mass'])) + + fh.write("\n") + + if player['ghosts'] == "yes" or player['lps'] == "yes": + fh.write("\n" + "------------------------------------------------------------------------------------------\n" + " Aditional potential parameters:\n" + "------------------------------------------------------------------------------------------\n") + + if player['ghosts'] == "yes": + + fh.write("\n") + fh.write("{} ghost atoms appended to molecule type 1 at:\n".format(len(ghost_types))) + fh.write("---------------------------------------------------------------------------------\n") + + atoms_string = "" + for ghost in ghost_types: + for atom in ghost['numbers']: + atom_sym = atomsymb[ molecules[0][atom - 1]['na'] ].strip() + atoms_string += "{}{} ".format(atom_sym,atom) + + if ghost['type'] == "g": + fh.write(textwrap.fill("* Geometric center of atoms {}".format(atoms_string), 80)) + elif ghost['type'] == "m": + fh.write(textwrap.fill("* Center of mass of atoms {}".format(atoms_string), 80)) + elif ghost['type'] == "z": + fh.write(textwrap.fill("* Center of atomic number of atoms {}".format(atoms_string), 80)) + + fh.write("\n") + + if player['lps'] == 'yes': + + fh.write("\n") + fh.write("{} lone pairs appended to molecule type 1:\n".format(len(lp_types))) + fh.write("---------------------------------------------------------------------------------\n") + + for lp in lp_types: + # LP type 1 or 2 + if lp['type'] in (1, 2): + atom1_num = lp['numbers'][0] + atom1_sym = atomsymb[ molecules[0][atom1_num - 1]['na'] ].strip() + atom2_num = lp['numbers'][1] + atom2_sym = atomsymb[ molecules[0][atom2_num - 1]['na'] ].strip() + atom3_num = lp['numbers'][2] + atom3_sym = atomsymb[ molecules[0][atom3_num - 1]['na'] ].strip() + + fh.write(textwrap.fill( + "* Type {} on atom {}{} with {}{} {}{}. Alpha = {:<5.1f} Deg and D = {:<4.2f} Angs".format( + lp['type'], atom1_sym, atom1_num, atom2_sym, atom2_num, atom3_sym, atom3_num, lp['alpha'], + lp['dist']), 86)) + fh.write("\n") + + # Other LP types + + fh.write("\n" + "==========================================================================================\n") + + return + +## Creation of continue_function + +def check_executables(fh): + + fh.write("\n") + fh.write(90 * "=") + fh.write("\n\n") + + dice_path = shutil.which(dice['progname']) + if dice_path != None: + fh.write("Program {} found at {}\n".format(dice['progname'], dice_path)) + else: + sys.exit("Error: cannot find dice executable") + + qmprog_path = shutil.which(player['qmprog']) + if qmprog_path != None: + fh.write("Program {} found at {}\n".format(player['qmprog'], qmprog_path)) + else: + sys.exit("Error: cannot find {} executable".format(player['qmprog'])) + + if player['qmprog'] in ("g03", "g09", "g16"): + formchk_path = shutil.which("formchk") + if formchk_path != None: + fh.write("Program formchk found at {}\n".format(formchk_path)) + else: + sys.exit("Error: cannot find formchk executable") + + + return + + + diff --git a/DPpack/__init__.py b/DPpack/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/DPpack/__pycache__/Dice.cpython-36.pyc b/DPpack/__pycache__/Dice.cpython-36.pyc new file mode 100644 index 0000000000000000000000000000000000000000..b636689574d993f346efb66b17224c518a49dee9 GIT binary patch literal 12358 zcmds7%WoV#yv zJ;UmzM7C$*0924uHVTkGU=KlnT!O@ZK#)TMZu!kHBY@FZsRZq`@ z)XN(KiAhXVb-lW(y1rk1-|wsI6BF)Vyz|Z{_HSz1ziC5%2GZ}~7yJ_fp$WaIRaC53 zbbdA}2FGT_L~JyzR;H5CsgBvSTiHsM(^k{DLwQy+m&7jOOeHVQRth3pnGjB;D00Gm zs8uFKUK9|Q#Dpj!o)VLygm_v^iD|^g#4$00ct#u-vxtw2IWdoTRxF4Ui08zjSVBB6 zUJ@q}FNjm3jQE5&EzTfb6#9qS^0~*Dk+!z1$Byv4POaV9N7|NEU$k3D>6fFa_k2-q zZuvurt;g0sl>b_8|LK=+H%&Z!_4!wyn_7(u=r4<(h2Qt_3mhGbrZ=>% zcA)nRVIZX=Wp<5FZy0l0*PPROR%kZN1Fe_oW>NIZdLQ0lhi=#E+6M;e4`2dMk?FwVAjL%-VcB6nqPKU!&4gYZh6 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0000000..98a38a1 --- /dev/null +++ b/control.in @@ -0,0 +1,21 @@ +# diceplayer +initcyc = 1 +maxcyc = 3 +opt = NO +nprocs = 2 +qmprog = g09 +lps = no +ghosts = no +altsteps = 20000 + +# dice +ncores = 1 +nmol = 1 100 +dens = 0.75 +nstep = 40000 60000 50000 +isave = 1000 +ljname = phb.pot +outname = phb + +# Gaussian +level = MP2/aug-cc-pVTZ diff --git a/diceplayer-0.0.1.py b/diceplayer-0.0.1.py new file mode 100644 index 0000000..e9cb51e --- /dev/null +++ b/diceplayer-0.0.1.py @@ -0,0 +1,295 @@ +#!/export/apps/python/361/bin/python3 + +import os, sys, time, signal +import argparse +import shutil +from multiprocessing import Process, connection + +import DPpack.Dice as Dice +import DPpack.Gaussian as Gaussian +from DPpack.PTable import * +from DPpack.SetGlobals import * +from DPpack.MolHandling import * +from DPpack.Misc import * + + +if __name__ == '__main__': +#### Read and store the arguments passed to the program #### +#### and set the usage and help messages #### + + parser = argparse.ArgumentParser(prog='Diceplayer') + parser.add_argument('--version', action='version', version='%(prog)s 1.0') + parser.add_argument('-i', dest='infile', default='control.in', metavar='INFILE', + help='input file of diceplayer [default = control.in]') + parser.add_argument('-o', dest='outfile', default='run.log', metavar='OUTFILE', + help='output file of diceplayer [default = run.log]') + + args = parser.parse_args() + +#### Read and check the keywords in INFILE + + read_keywords(args.infile) + check_keywords(args.infile) + +#### Open OUTFILE for writing and print keywords and initial info + + try: + if player['initcyc'] > 1 and os.path.exists(args.outfile): + oldname = args.outfile + ".old" + os.replace(args.outfile, oldname) + logfh = open(args.outfile, 'w', 1) + except EnvironmentError as err: + sys.exit(err) + + print_keywords(logfh) + +#### Check whether the executables are in the path + + check_executables(logfh) + +#### Read the potential, store the info in 'molecules' and prints the info in OUTFILE + + read_potential(args.infile) + + if player['lps'] == "yes": + read_lps() + + if player['ghosts'] == "yes": + read_ghosts() + + print_potential(logfh) + +#### Bring the molecules to standard orientation and prints info about them + + for i in range(len(molecules)): + logfh.write("\nMolecule type {}:\n\n".format(i + 1)) + print_mol_info(molecules[i], logfh) + logfh.write(" Translating and rotating molecule to standard orientation...") + standard_orientation(molecules[i]) + logfh.write(" Done\n\n New values:\n") + print_mol_info(molecules[i], logfh) + + logfh.write(90 * "=") + logfh.write("\n") + +#### Open the geoms.xyz file and prints the initial geometry if starting from zero + + if player['initcyc'] == 1: + try: + geomsfh = open("geoms.xyz", "w", 1) + except EnvironmentError as err: + sys.exit(err) + print_geom(0, geomsfh) + else: + try: + geomsfh = open("geoms.xyz", "A", 1) + except EnvironmentError as err: + sys.exit(err) + + + logfh.write("\nStarting the iterative process.\n") + + ## Initial position (in Bohr) + position = read_position(molecules[0]) + + ## If restarting, read the last gradient and hessian + if player['initcyc'] > 1: + if player['qmprog'] in ("g03", "g09", "g16"): + Gaussian.read_forces("grad_hessian.dat") + Gaussian.read_hessian_fchk("grad_hessian.dat") + + #if player['qmprog'] == "molcas": + #Molcas.read_forces("grad_hessian.dat") + #Molcas.read_hessian("grad_hessian.dat") + + #### + #### Start the iterative process + #### + + for cycle in range(player['initcyc'], player['initcyc'] + player['maxcyc']): + + logfh.write("\n" + 90 * "-" + "\n") + logfh.write("{} Step # {}\n".format(40 * " ", cycle)) + logfh.write(90 * "-" + "\n\n") + + make_step_dir(cycle) + + if player['altsteps'] == 0 or cycle == 1: + dice['randominit'] = True + else: + dice['randominit'] = False + + #### + #### Start block of parallel simulations + #### + + procs = [] + sentinels = [] + for proc in range(1, player['nprocs'] + 1): + + p = Process(target=Dice.simulation_process, args=(cycle, proc, logfh)) + p.start() + procs.append(p) + sentinels.append(p.sentinel) + + while procs: + finished = connection.wait(sentinels) + for proc_sentinel in finished: + i = sentinels.index(proc_sentinel) + status = procs[i].exitcode + procs.pop(i) + sentinels.pop(i) + if status != 0: + for p in procs: + p.terminate() + sys.exit(status) + + for proc in range(1, player['nprocs'] + 1): + Dice.print_last_config(cycle, proc) + + #### + #### End of parallel simulations block + #### + + ## Make ASEC + logfh.write("\nBuilding the ASEC and vdW meanfields... ") + asec_charges = populate_asec_vdw(cycle, logfh) + + ## After ASEC is built, compress files bigger than 1MB + for proc in range(1, player['nprocs'] + 1): + path = "step{:02d}".format(cycle) + os.sep + "p{:02d}".format(proc) + compress_files_1mb(path) + + #### + #### Start QM calculation + #### + + make_qm_dir(cycle) + + if player['opt'] == "yes": + + ## + ## Gaussian block + ## + if player['qmprog'] in ("g03", "g09", "g16"): + + if cycle > 1: + src = "step{:02d}".format(cycle - 1) + os.sep + "qm" + os.sep + "asec.chk" + dst = "step{:02d}".format(cycle) + os.sep + "qm" + os.sep + "asec.chk" + shutil.copyfile(src, dst) + + Gaussian.make_force_input(cycle, asec_charges) + Gaussian.run_gaussian(cycle, "force", logfh) + Gaussian.run_formchk(cycle, logfh) + + ## Read the gradient + file = "step{:02d}".format(cycle) + os.sep + "qm" + os.sep + "asec.fchk" + gradient = Gaussian.read_forces(file, logfh) + if len(cur_gradient) > 0: + old_gradient = cur_gradient + cur_gradient = gradient + + ## If 1st step, read the hessian + if cycle == 1: + if player['readhessian'] == "yes": + file = "grad_hessian.dat" + logfh.write("\nReading the hessian matrix from file {}\n".format(file)) + hessian = Gaussian.read_hessian_fchk(file) + else: + file = "step01" + os.sep + "qm" + os.sep + "asec.fchk" + logfh.write("\nReading the hessian matrix from file {}\n".format(file)) + hessian = Gaussian.read_hessian(file) + + ## From 2nd step on, update the hessian + else: + logfh.write("\nUpdating the hessian matrix using the BFGS method... ") + hessian = update_hessian(step, cur_gradient, old_gradient, hessian) + logfh.write("Done\n") + + ## Save gradient and hessian + Gaussian.print_grad_hessian(cycle, cur_gradient, hessian) + + ## Calculate the step and update the position + step = calculate_step(cur_gradient, hessian, logfh) + position += step + + ## Update the geometry of the reference molecule + update_molecule(position, logfh) + + ## If needed, calculate the charges + if cycle < player['switchcyc']: + + Gaussian.make_charge_input(cycle, asec_charges) + Gaussian.run_gaussian(cycle, "charge", logfh) + + ## Read the new charges and update molecules[0] + if cycle < player['switchcyc']: + file = "step{:02d}".format(cycle) + os.sep + "qm" + os.sep + "asec2.log" + Gaussian.read_charges(file, logfh) + else: + file = "step{:02d}".format(cycle) + os.sep + "qm" + os.sep + "asec.log" + Gaussian.read_charges(file, logfh) + + ## Print new info for molecule[0] + logfh.write("\nNew values for molecule type 1:\n\n") + print_mol_info(molecules[0], logfh) + + ## Print new geometry in geoms.xyz + print_geom(cycle, geomsfh) + + ## + ## Molcas block + ## + #if player['qmprog'] == "molcas": + + + #elif player['opt'] == "ts": + + ## + ## Gaussian block + ## + #if player['qmprog'] in ("g03", "g09", "g16"): + + + + ## + ## Molcas block + ## + #if player['qmprog'] == "molcas": + + + else: ## Only relax the charge distribution + + if player['qmprog'] in ("g03", "g09", "g16"): + + if cycle > 1: + src = "step{:02d}".format(cycle - 1) + os.sep + "qm" + os.sep + "asec.chk" + dst = "step{:02d}".format(cycle) + os.sep + "qm" + os.sep + "asec.chk" + shutil.copyfile(src, dst) + + Gaussian.make_charge_input(cycle, asec_charges) + Gaussian.run_gaussian(cycle, "charge", logfh) + + file = "step{:02d}".format(cycle) + os.sep + "qm" + os.sep + "asec2.log" + Gaussian.read_charges(file) + + ## Print new info for molecule[0] + logfh.write("\nNew values for molecule type 1:\n\n") + print_mol_info(molecules[0], logfh) + + #if player['qmprog'] == "molcas": + + + + #### + #### End of the iterative process + #### + +## imprimir ultimas mensagens, criar um arquivo de potencial para ser usado em eventual +## continuacao, fechar arquivos (geoms.xyz, run.log, ...) + + logfh.write("\nDiceplayer finished normally!\n") + logfh.close() +#### +#### End of the program +#### \ No newline at end of file diff --git a/geoms.xyz b/geoms.xyz new file mode 100644 index 0000000..74643c1 --- /dev/null +++ b/geoms.xyz @@ -0,0 +1,33 @@ +31 +Cycle # 0 +C -4.394497 0.698769 0.421354 +C -4.504613 -0.640849 -0.141092 +C -3.266831 -1.267916 -0.601745 +C -2.064301 -0.654971 -0.479838 +C -1.966148 0.666069 0.106967 +C -3.195469 1.321761 0.499266 +O -5.604026 -1.213715 -0.270977 +N -0.863607 1.365979 0.273247 +C 0.394047 0.812820 0.140269 +C 1.418955 1.646567 -0.341744 +C 0.757396 -0.471466 0.587991 +C 2.717900 1.193894 -0.471504 +C 2.068121 -0.911914 0.507136 +C 3.079906 -0.111825 -0.067434 +N 4.367937 -0.572075 -0.209272 +C 5.421862 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-4.34905 + C -1.73632 0.31775 -3.95112 + C -1.00588 1.46775 -3.62865 + C 0.38422 1.45395 -3.70592 + C 1.05166 0.29016 -4.10604 + H 0.84000 -1.75139 -4.73543 + H -1.63603 -1.72685 -4.59783 + H -1.52069 2.36555 -3.31999 + H 2.12991 0.27949 -4.16598 + O 1.09380 2.57108 -3.39267 + H 0.48990 3.27349 -3.14064 + C -3.24393 0.33268 -3.86732 + H -3.60255 1.32067 -4.06782 + H -3.64797 -0.34663 -4.58855 + H -3.54956 0.03464 -2.88617 + C 0.32520 -0.85357 -4.42675 + C -1.07260 -0.83969 -4.34906 + C -1.73632 0.31774 -3.95111 + C -1.00591 1.46774 -3.62866 + C 0.38426 1.45396 -3.70591 + C 1.05165 0.29017 -4.10605 + H 0.84000 -1.75144 -4.73544 + H -1.63608 -1.72689 -4.59780 + H -1.52070 2.36553 -3.31997 + H 2.12996 0.27948 -4.16600 + O 1.09380 2.57106 -3.39269 + H 0.48989 3.27347 -3.14061 + C -3.24393 0.33268 -3.86732 + H -3.60246 1.32067 -4.06787 + H -3.64796 -0.34665 -4.58852 + H -3.54955 0.03462 -2.88619 + C 0.32520 -0.85357 -4.42676 + C -1.07259 -0.83972 -4.34907 + C -1.73632 0.31775 -3.95110 + C -1.00590 1.46774 -3.62865 + C 0.38424 1.45396 -3.70591 + C 1.05168 0.29015 -4.10603 + H 0.84001 -1.75140 -4.73544 + H -1.63604 -1.72685 -4.59783 + H -1.52071 2.36556 -3.31998 + H 2.12996 0.27950 -4.16599 + O 1.09378 2.57108 -3.39271 + H 0.48987 3.27350 -3.14065 + C -3.24393 0.33269 -3.86730 + H -3.60249 1.32067 -4.06783 + H -3.64800 -0.34660 -4.58853 + H -3.54955 0.03464 -2.88622 + C 0.32519 -0.85359 -4.42675 + C -1.07259 -0.83972 -4.34907 + C -1.73632 0.31775 -3.95111 + C -1.00589 1.46775 -3.62864 + C 0.38423 1.45396 -3.70592 + C 1.05167 0.29015 -4.10605 + H 0.84001 -1.75140 -4.73543 + H -1.63610 -1.72684 -4.59780 + H -1.52071 2.36557 -3.31997 + H 2.12998 0.27951 -4.16598 + O 1.09381 2.57110 -3.39268 + H 0.48988 3.27346 -3.14063 + C -3.24396 0.33266 -3.86732 + H -3.60252 1.32068 -4.06784 + H -3.64798 -0.34664 -4.58853 + H -3.54963 0.03460 -2.88617 + C 0.32519 -0.85356 -4.42673 + C -1.07259 -0.83974 -4.34905 + C -1.73634 0.31773 -3.95111 + C -1.00590 1.46774 -3.62865 + C 0.38424 1.45396 -3.70593 + C 1.05166 0.29015 -4.10604 + H 0.83999 -1.75138 -4.73543 + H -1.63606 -1.72685 -4.59782 + H -1.52070 2.36554 -3.31998 + H 2.12997 0.27948 -4.16599 + O 1.09381 2.57109 -3.39269 + H 0.48988 3.27345 -3.14062 + C -3.24392 0.33269 -3.86732 + H -3.60253 1.32068 -4.06784 + H -3.64798 -0.34663 -4.58854 + H -3.54956 0.03460 -2.88618 + C 0.32519 -0.85357 -4.42676 + C -1.07258 -0.83970 -4.34905 + C -1.73629 0.31777 -3.95113 + C -1.00588 1.46774 -3.62865 + C 0.38421 1.45394 -3.70593 + C 1.05165 0.29018 -4.10605 + H 0.83999 -1.75137 -4.73542 + H -1.63608 -1.72684 -4.59781 + H -1.52070 2.36556 -3.31997 + H 2.12993 0.27950 -4.16597 + O 1.09377 2.57105 -3.39267 + H 0.48988 3.27341 -3.14065 + C -3.24392 0.33269 -3.86729 + H -3.60250 1.32065 -4.06786 + H -3.64791 -0.34664 -4.58852 + H -3.54954 0.03464 -2.88618 + C 0.32518 -0.85356 -4.42674 + C -1.07259 -0.83972 -4.34905 + C -1.73634 0.31774 -3.95111 + C -1.00590 1.46774 -3.62865 + C 0.38424 1.45395 -3.70593 + C 1.05168 0.29017 -4.10605 + H 0.83998 -1.75137 -4.73544 + H -1.63605 -1.72686 -4.59782 + H -1.52069 2.36555 -3.31998 + H 2.12994 0.27950 -4.16593 + O 1.09379 2.57107 -3.39269 + H 0.48990 3.27350 -3.14062 + C -3.24393 0.33268 -3.86732 + H -3.60246 1.32063 -4.06783 + H -3.64794 -0.34661 -4.58853 + H -3.54960 0.03463 -2.88615 + C 0.32519 -0.85357 -4.42675 + C -1.07259 -0.83973 -4.34907 + C -1.73632 0.31775 -3.95110 + C -1.00590 1.46774 -3.62864 + C 0.38422 1.45396 -3.70593 + C 1.05168 0.29015 -4.10606 + H 0.83994 -1.75142 -4.73543 + H -1.63607 -1.72684 -4.59781 + H -1.52072 2.36555 -3.31998 + H 2.12995 0.27949 -4.16598 + O 1.09379 2.57109 -3.39267 + H 0.48989 3.27350 -3.14063 + C -3.24391 0.33268 -3.86731 + H -3.60250 1.32067 -4.06784 + H -3.64794 -0.34665 -4.58853 + H -3.54956 0.03461 -2.88620 diff --git a/new_cyclo.xyz.new2 b/new_cyclo.xyz.new2 new file mode 100644 index 0000000..dd0ca8a --- /dev/null +++ b/new_cyclo.xyz.new2 @@ -0,0 +1,1782 @@ +16 + Configuration number : 50000L = 26.5871 26.5871 26.5871 + C 0.32518 -0.85357 -4.42676 + C -1.07260 -0.83974 -4.34908 + C -1.73631 0.31774 -3.95110 + C -1.00591 1.46774 -3.62865 + C 0.38423 1.45395 -3.70591 + C 1.05166 0.29016 -4.10605 + H 0.83995 -1.75138 -4.73542 + H -1.63606 -1.72686 -4.59780 + H -1.52070 2.36556 -3.31997 + H 2.12991 0.27949 -4.16599 + O 1.09380 2.57109 -3.39268 + H 0.48988 3.27349 -3.14062 + C -3.24390 0.33270 -3.86732 + H -3.60253 1.32066 -4.06786 + H -3.64797 -0.34663 -4.58853 + H -3.54955 0.03462 -2.88619 +16 + Configuration number : 50000L = 26.5871 26.5871 26.5871 + C 0.32518 -0.85355 -4.42673 + C -1.07259 -0.83973 -4.34908 + C -1.73629 0.31775 -3.95111 + C -1.00591 1.46772 -3.62865 + C 0.38426 1.45397 -3.70591 + C 1.05167 0.29016 -4.10605 + H 0.83998 -1.75141 -4.73542 + H -1.63606 -1.72684 -4.59780 + H -1.52071 2.36556 -3.31997 + H 2.12995 0.27950 -4.16599 + O 1.09380 2.57108 -3.39269 + H 0.48991 3.27347 -3.14062 + C -3.24396 0.33270 -3.86732 + H -3.60249 1.32065 -4.06785 + H -3.64803 -0.34666 -4.58855 + H -3.54959 0.03460 -2.88617 +16 + Configuration number : 50000L = 26.5871 26.5871 26.5871 + C 0.32519 -0.85358 -4.42676 + C -1.07258 -0.83969 -4.34907 + C -1.73630 0.31774 -3.95111 + C -1.00589 1.46775 -3.62865 + C 0.38424 1.45395 -3.70592 + C 1.05164 0.29017 -4.10605 + H 0.83997 -1.75140 -4.73543 + H -1.63608 -1.72689 -4.59781 + H -1.52070 2.36555 -3.31997 + H 2.12995 0.27949 -4.16599 + O 1.09380 2.57107 -3.39267 + H 0.48988 3.27345 -3.14065 + C -3.24393 0.33268 -3.86731 + H -3.60250 1.32066 -4.06785 + H -3.64797 -0.34665 -4.58855 + H -3.54958 0.03462 -2.88617 +16 + Configuration number : 50000L = 26.5871 26.5871 26.5871 + C 0.32518 -0.85357 -4.42674 + C -1.07259 -0.83973 -4.34907 + C -1.73632 0.31775 -3.95111 + C -1.00590 1.46774 -3.62865 + C 0.38421 1.45395 -3.70592 + C 1.05169 0.29017 -4.10605 + H 0.84000 -1.75141 -4.73545 + H -1.63607 -1.72689 -4.59781 + H -1.52071 2.36555 -3.31997 + H 2.12990 0.27947 -4.16599 + O 1.09379 2.57109 -3.39269 + H 0.48992 3.27350 -3.14062 + C -3.24391 0.33268 -3.86731 + H -3.60249 1.32066 -4.06787 + H -3.64792 -0.34663 -4.58854 + H -3.54957 0.03462 -2.88617 +16 + Configuration number : 50000L = 26.5871 26.5871 26.5871 + C 0.32518 -0.85360 -4.42674 + C -1.07258 -0.83972 -4.34906 + C -1.73632 0.31775 -3.95112 + C -1.00588 1.46774 -3.62865 + C 0.38423 1.45397 -3.70592 + C 1.05166 0.29017 -4.10605 + H 0.83998 -1.75144 -4.73545 + H -1.63604 -1.72684 -4.59784 + H -1.52071 2.36561 -3.31996 + H 2.12994 0.27951 -4.16599 + O 1.09378 2.57109 -3.39267 + H 0.48990 3.27353 -3.14062 + C -3.24393 0.33268 -3.86731 + H -3.60247 1.32067 -4.06787 + H -3.64793 -0.34664 -4.58853 + H -3.54951 0.03465 -2.88617 +16 + Configuration number : 50000L = 26.5871 26.5871 26.5871 + C 0.32515 -0.85356 -4.42674 + C -1.07259 -0.83973 -4.34904 + C -1.73630 0.31775 -3.95110 + C -1.00589 1.46774 -3.62865 + C 0.38421 1.45396 -3.70594 + C 1.05166 0.29017 -4.10604 + H 0.83998 -1.75140 -4.73546 + H -1.63608 -1.72684 -4.59779 + H -1.52069 2.36556 -3.31998 + H 2.12995 0.27950 -4.16599 + O 1.09377 2.57106 -3.39269 + H 0.48990 3.27348 -3.14062 + C -3.24387 0.33268 -3.86732 + H -3.60246 1.32067 -4.06785 + H -3.64792 -0.34664 -4.58857 + H -3.54951 0.03462 -2.88619 +16 + Configuration number : 50000L = 26.5871 26.5871 26.5871 + C 0.32519 -0.85357 -4.42675 + C -1.07261 -0.83973 -4.34905 + C -1.73632 0.31775 -3.95112 + C -1.00591 1.46775 -3.62866 + C 0.38422 1.45395 -3.70592 + C 1.05166 0.29017 -4.10605 + H 0.83998 -1.75141 -4.73546 + H -1.63608 -1.72685 -4.59781 + H -1.52070 2.36556 -3.31999 + H 2.12995 0.27948 -4.16601 + O 1.09379 2.57109 -3.39267 + H 0.48987 3.27348 -3.14065 + C -3.24388 0.33267 -3.86731 + H -3.60251 1.32069 -4.06785 + H -3.64794 -0.34662 -4.58854 + H -3.54960 0.03460 -2.88617 +16 + Configuration number : 50000L = 26.5871 26.5871 26.5871 + C 0.32518 -0.85358 -4.42676 + C -1.07259 -0.83970 -4.34905 + C -1.73632 0.31774 -3.95110 + C -1.00590 1.46773 -3.62866 + C 0.38423 1.45395 -3.70593 + C 1.05167 0.29015 -4.10607 + H 0.84000 -1.75141 -4.73542 + H -1.63604 -1.72680 -4.59782 + H -1.52072 2.36557 -3.31995 + H 2.12996 0.27949 -4.16599 + O 1.09380 2.57108 -3.39267 + H 0.48987 3.27355 -3.14065 + C -3.24393 0.33270 -3.86730 + H -3.60250 1.32068 -4.06784 + H -3.64797 -0.34665 -4.58854 + H -3.54962 0.03462 -2.88618 +16 + Configuration number : 50000L = 26.5871 26.5871 26.5871 + C 0.32518 -0.85357 -4.42674 + C -1.07258 -0.83971 -4.34906 + C -1.73634 0.31774 -3.95111 + C -1.00588 1.46774 -3.62865 + C 0.38421 1.45395 -3.70593 + C 1.05167 0.29015 -4.10606 + H 0.83997 -1.75137 -4.73543 + H -1.63608 -1.72683 -4.59782 + H -1.52072 2.36558 -3.31997 + H 2.12994 0.27948 -4.16598 + O 1.09383 2.57110 -3.39267 + H 0.48990 3.27348 -3.14065 + C -3.24394 0.33266 -3.86731 + H -3.60253 1.32066 -4.06786 + H -3.64794 -0.34665 -4.58853 + H -3.54956 0.03461 -2.88619 +16 + Configuration number : 50000L = 26.5871 26.5871 26.5871 + C 0.32517 -0.85357 -4.42676 + C -1.07261 -0.83974 -4.34907 + C -1.73633 0.31774 -3.95112 + C -1.00591 1.46775 -3.62865 + C 0.38423 1.45396 -3.70592 + C 1.05166 0.29015 -4.10606 + H 0.83997 -1.75141 -4.73543 + H -1.63606 -1.72687 -4.59781 + H -1.52072 2.36559 -3.31997 + H 2.12995 0.27949 -4.16600 + O 1.09382 2.57110 -3.39266 + H 0.48988 3.27351 -3.14061 + C -3.24390 0.33269 -3.86732 + H -3.60251 1.32068 -4.06787 + H -3.64796 -0.34664 -4.58852 + H -3.54958 0.03460 -2.88618 +16 + Configuration number : 50000L = 26.5871 26.5871 26.5871 + C 0.32516 -0.85358 -4.42677 + C -1.07261 -0.83973 -4.34906 + C -1.73633 0.31774 -3.95111 + C -1.00588 1.46775 -3.62866 + C 0.38424 1.45394 -3.70593 + C 1.05165 0.29017 -4.10603 + H 0.83998 -1.75139 -4.73546 + H -1.63606 -1.72684 -4.59782 + H -1.52070 2.36556 -3.31998 + H 2.12993 0.27950 -4.16600 + O 1.09381 2.57108 -3.39267 + H 0.48992 3.27350 -3.14066 + C -3.24391 0.33269 -3.86732 + H -3.60248 1.32064 -4.06787 + H -3.64796 -0.34666 -4.58854 + H -3.54956 0.03462 -2.88619 +16 + Configuration number : 50000L = 26.5871 26.5871 26.5871 + C 0.32519 -0.85359 -4.42674 + C -1.07259 -0.83970 -4.34907 + C -1.73632 0.31775 -3.95109 + C -1.00591 1.46775 -3.62866 + C 0.38424 1.45396 -3.70591 + C 1.05168 0.29015 -4.10605 + H 0.83996 -1.75138 -4.73544 + H -1.63607 -1.72684 -4.59781 + H -1.52068 2.36559 -3.31999 + H 2.12994 0.27948 -4.16597 + O 1.09376 2.57107 -3.39268 + H 0.48986 3.27347 -3.14063 + C -3.24388 0.33269 -3.86734 + H -3.60246 1.32064 -4.06783 + H -3.64798 -0.34663 -4.58852 + H -3.54961 0.03460 -2.88617 +16 + Configuration number : 50000L = 26.5871 26.5871 26.5871 + C 0.32517 -0.85356 -4.42675 + C -1.07259 -0.83968 -4.34907 + C -1.73632 0.31774 -3.95111 + C -1.00590 1.46773 -3.62865 + C 0.38424 1.45395 -3.70592 + C 1.05165 0.29016 -4.10605 + H 0.83997 -1.75138 -4.73542 + H -1.63606 -1.72686 -4.59779 + H -1.52069 2.36554 -3.31997 + H 2.12995 0.27950 -4.16596 + O 1.09375 2.57107 -3.39269 + H 0.48986 3.27342 -3.14063 + C -3.24385 0.33268 -3.86731 + H -3.60245 1.32068 -4.06785 + H -3.64792 -0.34661 -4.58852 + H -3.54952 0.03463 -2.88618 +16 + Configuration number : 50000L = 26.5871 26.5871 26.5871 + C 0.32518 -0.85358 -4.42676 + C -1.07258 -0.83972 -4.34906 + C -1.73631 0.31774 -3.95110 + C -1.00590 1.46775 -3.62865 + C 0.38422 1.45396 -3.70592 + C 1.05167 0.29016 -4.10606 + H 0.84001 -1.75143 -4.73545 + H -1.63605 -1.72686 -4.59781 + H -1.52073 2.36559 -3.31995 + H 2.12995 0.27948 -4.16599 + O 1.09378 2.57109 -3.39268 + H 0.48989 3.27349 -3.14063 + C -3.24391 0.33267 -3.86731 + H -3.60253 1.32068 -4.06788 + H -3.64796 -0.34661 -4.58853 + H -3.54963 0.03462 -2.88614 +16 + Configuration number : 50000L = 26.5871 26.5871 26.5871 + C 0.32520 -0.85358 -4.42675 + C -1.07258 -0.83973 -4.34903 + C -1.73632 0.31776 -3.95111 + C -1.00589 1.46774 -3.62865 + C 0.38423 1.45395 -3.70592 + C 1.05167 0.29016 -4.10606 + H 0.83998 -1.75139 -4.73543 + H -1.63607 -1.72687 -4.59781 + H -1.52071 2.36556 -3.31998 + H 2.12995 0.27950 -4.16597 + O 1.09381 2.57109 -3.39269 + H 0.48990 3.27348 -3.14060 + C -3.24397 0.33268 -3.86732 + H -3.60256 1.32068 -4.06785 + H -3.64798 -0.34663 -4.58855 + H -3.54955 0.03462 -2.88616 +16 + Configuration number : 50000L = 26.5871 26.5871 26.5871 + C 0.32518 -0.85359 -4.42675 + C -1.07260 -0.83972 -4.34907 + C -1.73631 0.31775 -3.95111 + C -1.00590 1.46775 -3.62865 + C 0.38423 1.45395 -3.70590 + C 1.05166 0.29016 -4.10605 + H 0.83999 -1.75137 -4.73542 + H -1.63607 -1.72684 -4.59781 + H -1.52069 2.36555 -3.31997 + H 2.12996 0.27947 -4.16598 + O 1.09380 2.57109 -3.39268 + H 0.48989 3.27348 -3.14063 + C -3.24391 0.33268 -3.86733 + H -3.60251 1.32067 -4.06784 + H -3.64798 -0.34664 -4.58855 + H -3.54955 0.03461 -2.88617 +16 + Configuration number : 50000L = 26.5871 26.5871 26.5871 + C 0.32517 -0.85357 -4.42675 + C -1.07260 -0.83972 -4.34907 + C -1.73632 0.31773 -3.95112 + C -1.00589 1.46774 -3.62866 + C 0.38424 1.45397 -3.70591 + C 1.05166 0.29016 -4.10604 + H 0.83995 -1.75138 -4.73541 + H -1.63609 -1.72688 -4.59782 + H -1.52071 2.36555 -3.31997 + H 2.12991 0.27950 -4.16596 + O 1.09379 2.57109 -3.39268 + H 0.48990 3.27351 -3.14061 + C -3.24389 0.33267 -3.86732 + H -3.60254 1.32068 -4.06783 + H -3.64796 -0.34664 -4.58850 + H -3.54958 0.03461 -2.88619 +16 + Configuration number : 50000L = 26.5871 26.5871 26.5871 + C 0.32520 -0.85358 -4.42675 + C -1.07259 -0.83974 -4.34907 + C -1.73632 0.31775 -3.95112 + C -1.00588 1.46775 -3.62865 + C 0.38422 1.45396 -3.70592 + C 1.05168 0.29018 -4.10604 + H 0.83999 -1.75138 -4.73542 + H -1.63607 -1.72685 -4.59783 + H -1.52069 2.36557 -3.32000 + H 2.12998 0.27949 -4.16596 + O 1.09379 2.57107 -3.39268 + H 0.48988 3.27353 -3.14065 + C -3.24395 0.33268 -3.86731 + H -3.60248 1.32067 -4.06780 + H -3.64798 -0.34660 -4.58854 + H -3.54956 0.03460 -2.88618 +16 + Configuration number : 50000L = 26.5871 26.5871 26.5871 + C 0.32518 -0.85359 -4.42676 + C -1.07260 -0.83976 -4.34906 + C -1.73631 0.31775 -3.95110 + C -1.00589 1.46773 -3.62865 + C 0.38424 1.45396 -3.70591 + C 1.05168 0.29017 -4.10604 + H 0.84000 -1.75140 -4.73545 + H -1.63610 -1.72689 -4.59782 + H -1.52068 2.36555 -3.31997 + H 2.12999 0.27950 -4.16598 + O 1.09377 2.57109 -3.39269 + H 0.48988 3.27350 -3.14063 + C -3.24392 0.33271 -3.86732 + H -3.60254 1.32068 -4.06786 + H -3.64804 -0.34665 -4.58853 + H -3.54954 0.03462 -2.88619 +16 + Configuration number : 50000L = 26.5871 26.5871 26.5871 + C 0.32518 -0.85359 -4.42674 + C -1.07258 -0.83973 -4.34905 + C -1.73631 0.31776 -3.95111 + C -1.00590 1.46773 -3.62865 + C 0.38423 1.45396 -3.70593 + C 1.05166 0.29018 -4.10604 + H 0.83996 -1.75138 -4.73543 + H -1.63603 -1.72683 -4.59779 + H -1.52068 2.36556 -3.31996 + H 2.12994 0.27953 -4.16598 + O 1.09379 2.57108 -3.39269 + H 0.48991 3.27348 -3.14060 + C -3.24391 0.33269 -3.86732 + H -3.60252 1.32067 -4.06784 + H -3.64795 -0.34664 -4.58854 + H -3.54957 0.03464 -2.88618 +16 + Configuration number : 50000L = 26.5871 26.5871 26.5871 + C 0.32520 -0.85358 -4.42675 + C -1.07257 -0.83971 -4.34907 + C -1.73631 0.31774 -3.95110 + C -1.00588 1.46773 -3.62866 + C 0.38422 1.45395 -3.70591 + C 1.05166 0.29018 -4.10605 + H 0.83998 -1.75137 -4.73542 + H -1.63607 -1.72686 -4.59778 + H -1.52069 2.36556 -3.31997 + H 2.12992 0.27948 -4.16597 + O 1.09378 2.57109 -3.39267 + H 0.48987 3.27342 -3.14060 + C -3.24394 0.33268 -3.86733 + H -3.60254 1.32064 -4.06786 + H -3.64797 -0.34663 -4.58852 + H -3.54957 0.03464 -2.88615 +16 + Configuration number : 50000L = 26.5871 26.5871 26.5871 + C 0.32519 -0.85355 -4.42675 + C -1.07260 -0.83973 -4.34907 + C -1.73632 0.31773 -3.95110 + C -1.00589 1.46774 -3.62864 + C 0.38422 1.45395 -3.70594 + C 1.05166 0.29017 -4.10604 + H 0.83992 -1.75138 -4.73543 + H -1.63608 -1.72682 -4.59780 + H -1.52070 2.36557 -3.31998 + H 2.12994 0.27950 -4.16597 + O 1.09380 2.57108 -3.39268 + H 0.48987 3.27351 -3.14061 + C -3.24390 0.33268 -3.86733 + H -3.60250 1.32064 -4.06785 + H -3.64793 -0.34664 -4.58852 + H -3.54959 0.03463 -2.88617 +16 + Configuration number : 50000L = 26.5871 26.5871 26.5871 + C 0.32519 -0.85358 -4.42675 + C -1.07261 -0.83973 -4.34908 + C -1.73631 0.31774 -3.95112 + C -1.00590 1.46774 -3.62865 + C 0.38424 1.45396 -3.70592 + C 1.05167 0.29016 -4.10603 + H 0.83998 -1.75139 -4.73543 + H -1.63608 -1.72688 -4.59782 + H -1.52072 2.36558 -3.31996 + H 2.12996 0.27949 -4.16600 + O 1.09381 2.57109 -3.39267 + H 0.48991 3.27350 -3.14063 + C -3.24394 0.33269 -3.86731 + H -3.60251 1.32066 -4.06787 + H -3.64799 -0.34667 -4.58855 + H -3.54963 0.03462 -2.88613 +16 + Configuration number : 50000L = 26.5871 26.5871 26.5871 + C 0.32517 -0.85361 -4.42675 + C -1.07260 -0.83974 -4.34906 + C -1.73635 0.31774 -3.95111 + C -1.00589 1.46775 -3.62865 + C 0.38424 1.45395 -3.70593 + C 1.05167 0.29017 -4.10605 + H 0.83998 -1.75143 -4.73546 + H -1.63609 -1.72683 -4.59780 + H -1.52071 2.36558 -3.31996 + H 2.12997 0.27949 -4.16599 + O 1.09379 2.57111 -3.39267 + H 0.48988 3.27352 -3.14062 + C -3.24388 0.33269 -3.86732 + H -3.60254 1.32065 -4.06786 + H -3.64796 -0.34665 -4.58853 + H -3.54959 0.03462 -2.88619 +16 + Configuration number : 50000L = 26.5871 26.5871 26.5871 + C 0.32517 -0.85359 -4.42675 + C -1.07259 -0.83974 -4.34906 + C -1.73632 0.31774 -3.95110 + C -1.00588 1.46773 -3.62865 + C 0.38423 1.45396 -3.70593 + C 1.05165 0.29016 -4.10605 + H 0.83994 -1.75138 -4.73545 + H -1.63606 -1.72686 -4.59780 + H -1.52071 2.36558 -3.31998 + H 2.12992 0.27948 -4.16599 + O 1.09379 2.57110 -3.39268 + H 0.48987 3.27344 -3.14065 + C -3.24390 0.33271 -3.86730 + H -3.60248 1.32063 -4.06786 + H -3.64796 -0.34663 -4.58854 + H -3.54957 0.03458 -2.88622 +16 + Configuration number : 50000L = 26.5871 26.5871 26.5871 + C 0.32518 -0.85358 -4.42676 + C -1.07259 -0.83973 -4.34905 + C -1.73631 0.31776 -3.95111 + C -1.00589 1.46775 -3.62864 + C 0.38423 1.45396 -3.70593 + C 1.05167 0.29017 -4.10605 + H 0.84000 -1.75140 -4.73543 + H -1.63606 -1.72686 -4.59781 + H -1.52070 2.36557 -3.31994 + H 2.12996 0.27949 -4.16598 + O 1.09378 2.57107 -3.39267 + H 0.48990 3.27351 -3.14066 + C -3.24392 0.33269 -3.86734 + H -3.60251 1.32065 -4.06785 + H -3.64800 -0.34662 -4.58853 + H -3.54958 0.03461 -2.88617 +16 + Configuration number : 50000L = 26.5871 26.5871 26.5871 + C 0.32518 -0.85357 -4.42676 + C -1.07258 -0.83973 -4.34907 + C -1.73635 0.31774 -3.95111 + C -1.00590 1.46775 -3.62865 + C 0.38423 1.45396 -3.70590 + C 1.05168 0.29013 -4.10606 + H 0.84000 -1.75142 -4.73543 + H -1.63609 -1.72688 -4.59782 + H -1.52071 2.36557 -3.31997 + H 2.12995 0.27949 -4.16599 + O 1.09382 2.57111 -3.39268 + H 0.48987 3.27347 -3.14064 + C -3.24395 0.33268 -3.86732 + H -3.60248 1.32066 -4.06785 + H -3.64796 -0.34663 -4.58852 + H -3.54961 0.03460 -2.88616 +16 + Configuration number : 50000L = 26.5871 26.5871 26.5871 + C 0.32519 -0.85356 -4.42676 + C -1.07259 -0.83973 -4.34904 + C -1.73633 0.31775 -3.95111 + C -1.00589 1.46775 -3.62866 + C 0.38421 1.45394 -3.70592 + C 1.05165 0.29016 -4.10604 + H 0.84001 -1.75145 -4.73546 + H -1.63606 -1.72688 -4.59783 + H -1.52071 2.36559 -3.31996 + H 2.12991 0.27949 -4.16598 + O 1.09380 2.57108 -3.39269 + H 0.48988 3.27347 -3.14064 + C -3.24389 0.33269 -3.86731 + H -3.60251 1.32068 -4.06783 + H -3.64795 -0.34664 -4.58852 + H -3.54957 0.03462 -2.88620 +16 + Configuration number : 50000L = 26.5871 26.5871 26.5871 + C 0.32518 -0.85358 -4.42675 + C -1.07259 -0.83972 -4.34907 + C -1.73633 0.31774 -3.95112 + C -1.00590 1.46775 -3.62866 + C 0.38423 1.45395 -3.70592 + C 1.05165 0.29016 -4.10606 + H 0.83998 -1.75138 -4.73541 + H -1.63607 -1.72685 -4.59783 + H -1.52072 2.36556 -3.31996 + H 2.12988 0.27945 -4.16599 + O 1.09379 2.57110 -3.39266 + H 0.48984 3.27348 -3.14064 + C -3.24387 0.33268 -3.86732 + H -3.60252 1.32066 -4.06786 + H -3.64794 -0.34662 -4.58853 + H -3.54956 0.03465 -2.88615 +16 + Configuration number : 50000L = 26.5871 26.5871 26.5871 + C 0.32519 -0.85356 -4.42674 + C -1.07260 -0.83974 -4.34907 + C -1.73633 0.31775 -3.95110 + C -1.00589 1.46776 -3.62866 + C 0.38423 1.45397 -3.70593 + C 1.05167 0.29016 -4.10605 + H 0.83999 -1.75140 -4.73543 + H -1.63606 -1.72686 -4.59785 + H -1.52070 2.36558 -3.31997 + H 2.13001 0.27948 -4.16599 + O 1.09378 2.57106 -3.39270 + H 0.48988 3.27352 -3.14064 + C -3.24391 0.33267 -3.86730 + H -3.60250 1.32069 -4.06784 + H -3.64795 -0.34662 -4.58853 + H -3.54961 0.03461 -2.88618 +16 + Configuration number : 50000L = 26.5871 26.5871 26.5871 + C 0.32517 -0.85358 -4.42674 + C -1.07261 -0.83973 -4.34906 + C -1.73633 0.31774 -3.95110 + C -1.00589 1.46773 -3.62865 + C 0.38422 1.45396 -3.70592 + C 1.05167 0.29015 -4.10605 + H 0.84000 -1.75139 -4.73543 + H -1.63610 -1.72692 -4.59785 + H -1.52069 2.36556 -3.31997 + H 2.12998 0.27948 -4.16597 + O 1.09383 2.57112 -3.39269 + H 0.48990 3.27351 -3.14063 + C -3.24393 0.33268 -3.86733 + H -3.60245 1.32067 -4.06784 + H -3.64795 -0.34663 -4.58853 + H -3.54955 0.03459 -2.88618 +16 + Configuration number : 50000L = 26.5871 26.5871 26.5871 + C 0.32518 -0.85357 -4.42674 + C -1.07261 -0.83971 -4.34904 + C -1.73631 0.31775 -3.95111 + C -1.00590 1.46773 -3.62865 + C 0.38423 1.45395 -3.70592 + C 1.05165 0.29016 -4.10606 + H 0.83997 -1.75138 -4.73543 + H -1.63609 -1.72685 -4.59784 + H -1.52072 2.36554 -3.31999 + H 2.12989 0.27949 -4.16598 + O 1.09380 2.57108 -3.39270 + H 0.48989 3.27349 -3.14063 + C -3.24387 0.33267 -3.86732 + H -3.60251 1.32065 -4.06785 + H -3.64799 -0.34663 -4.58851 + H -3.54960 0.03460 -2.88621 +16 + Configuration number : 50000L = 26.5871 26.5871 26.5871 + C 0.32518 -0.85357 -4.42674 + C -1.07259 -0.83973 -4.34905 + C -1.73632 0.31774 -3.95112 + C -1.00589 1.46773 -3.62865 + C 0.38423 1.45396 -3.70590 + C 1.05165 0.29017 -4.10605 + H 0.83999 -1.75141 -4.73542 + H -1.63606 -1.72684 -4.59779 + H -1.52070 2.36558 -3.31995 + H 2.12994 0.27947 -4.16599 + O 1.09379 2.57109 -3.39269 + H 0.48993 3.27349 -3.14061 + C -3.24390 0.33269 -3.86734 + H -3.60248 1.32066 -4.06783 + H -3.64793 -0.34663 -4.58851 + H -3.54953 0.03460 -2.88621 +16 + Configuration number : 50000L = 26.5871 26.5871 26.5871 + C 0.32520 -0.85357 -4.42673 + C -1.07258 -0.83973 -4.34907 + C -1.73633 0.31776 -3.95110 + C -1.00590 1.46775 -3.62866 + C 0.38423 1.45394 -3.70592 + C 1.05168 0.29017 -4.10606 + H 0.84000 -1.75141 -4.73545 + H -1.63606 -1.72688 -4.59782 + H -1.52070 2.36558 -3.31998 + H 2.13000 0.27947 -4.16598 + O 1.09378 2.57107 -3.39268 + H 0.48989 3.27350 -3.14063 + C -3.24394 0.33269 -3.86731 + H -3.60250 1.32069 -4.06784 + H -3.64798 -0.34663 -4.58855 + H -3.54957 0.03460 -2.88616 +16 + Configuration number : 50000L = 26.5871 26.5871 26.5871 + C 0.32518 -0.85360 -4.42676 + C -1.07258 -0.83973 -4.34907 + C -1.73633 0.31775 -3.95110 + C -1.00589 1.46776 -3.62865 + C 0.38423 1.45395 -3.70592 + C 1.05169 0.29015 -4.10604 + H 0.83996 -1.75138 -4.73543 + H -1.63607 -1.72689 -4.59778 + H -1.52071 2.36560 -3.31996 + H 2.12993 0.27950 -4.16599 + O 1.09378 2.57111 -3.39267 + H 0.48994 3.27355 -3.14060 + C -3.24393 0.33268 -3.86733 + H -3.60254 1.32072 -4.06785 + H -3.64794 -0.34664 -4.58854 + H -3.54958 0.03458 -2.88616 +16 + Configuration number : 50000L = 26.5871 26.5871 26.5871 + C 0.32518 -0.85357 -4.42678 + C -1.07259 -0.83973 -4.34906 + C -1.73633 0.31774 -3.95110 + C -1.00588 1.46774 -3.62865 + C 0.38426 1.45395 -3.70591 + C 1.05166 0.29015 -4.10603 + H 0.83999 -1.75138 -4.73542 + H -1.63608 -1.72689 -4.59781 + H -1.52069 2.36560 -3.31998 + H 2.12995 0.27950 -4.16600 + O 1.09379 2.57110 -3.39268 + H 0.48991 3.27347 -3.14064 + C -3.24393 0.33270 -3.86732 + H -3.60248 1.32065 -4.06784 + H -3.64796 -0.34665 -4.58854 + H -3.54958 0.03460 -2.88620 +16 + Configuration number : 50000L = 26.5871 26.5871 26.5871 + C 0.32519 -0.85358 -4.42675 + C -1.07259 -0.83974 -4.34906 + C -1.73633 0.31774 -3.95111 + C -1.00589 1.46774 -3.62865 + C 0.38424 1.45395 -3.70592 + C 1.05166 0.29015 -4.10605 + H 0.84000 -1.75137 -4.73541 + H -1.63609 -1.72685 -4.59782 + H -1.52069 2.36558 -3.31997 + H 2.12994 0.27947 -4.16599 + O 1.09381 2.57112 -3.39268 + H 0.48989 3.27352 -3.14063 + C -3.24393 0.33268 -3.86732 + H -3.60252 1.32069 -4.06784 + H -3.64797 -0.34662 -4.58853 + H -3.54959 0.03457 -2.88618 +16 + Configuration number : 50000L = 26.5871 26.5871 26.5871 + C 0.32519 -0.85358 -4.42675 + C -1.07260 -0.83973 -4.34907 + C -1.73632 0.31774 -3.95111 + C -1.00590 1.46775 -3.62864 + C 0.38424 1.45395 -3.70593 + C 1.05167 0.29015 -4.10606 + H 0.83998 -1.75138 -4.73542 + H -1.63608 -1.72684 -4.59782 + H -1.52069 2.36560 -3.31997 + H 2.12994 0.27951 -4.16600 + O 1.09381 2.57110 -3.39267 + H 0.48989 3.27350 -3.14062 + C -3.24394 0.33269 -3.86731 + H -3.60246 1.32066 -4.06788 + H -3.64796 -0.34666 -4.58855 + H -3.54958 0.03461 -2.88614 +16 + Configuration number : 50000L = 26.5871 26.5871 26.5871 + C 0.32518 -0.85359 -4.42673 + C -1.07259 -0.83973 -4.34906 + C -1.73631 0.31775 -3.95111 + C -1.00588 1.46773 -3.62866 + C 0.38423 1.45395 -3.70592 + C 1.05165 0.29017 -4.10606 + H 0.84001 -1.75141 -4.73543 + H -1.63606 -1.72686 -4.59780 + H -1.52069 2.36557 -3.31996 + H 2.12991 0.27949 -4.16598 + O 1.09379 2.57108 -3.39269 + H 0.48990 3.27348 -3.14061 + C -3.24392 0.33270 -3.86731 + H -3.60248 1.32065 -4.06783 + H -3.64795 -0.34663 -4.58854 + H -3.54955 0.03462 -2.88619 +16 + Configuration number : 50000L = 26.5871 26.5871 26.5871 + C 0.32518 -0.85357 -4.42676 + C -1.07258 -0.83972 -4.34905 + C -1.73632 0.31774 -3.95111 + C -1.00591 1.46775 -3.62866 + C 0.38424 1.45396 -3.70591 + C 1.05166 0.29018 -4.10604 + H 0.83999 -1.75138 -4.73543 + H -1.63608 -1.72688 -4.59781 + H -1.52071 2.36557 -3.31997 + H 2.12989 0.27948 -4.16599 + O 1.09380 2.57107 -3.39269 + H 0.48987 3.27348 -3.14062 + C -3.24393 0.33268 -3.86732 + H -3.60246 1.32066 -4.06785 + H -3.64799 -0.34664 -4.58852 + H -3.54958 0.03463 -2.88618 +16 + Configuration number : 50000L = 26.5871 26.5871 26.5871 + C 0.32521 -0.85360 -4.42676 + C -1.07259 -0.83971 -4.34908 + C -1.73633 0.31775 -3.95110 + C -1.00591 1.46775 -3.62866 + C 0.38421 1.45394 -3.70591 + C 1.05166 0.29017 -4.10605 + H 0.83998 -1.75140 -4.73543 + H -1.63607 -1.72685 -4.59780 + H -1.52071 2.36557 -3.31997 + H 2.12994 0.27947 -4.16598 + O 1.09380 2.57109 -3.39267 + H 0.48988 3.27348 -3.14063 + C -3.24390 0.33268 -3.86731 + H -3.60253 1.32069 -4.06784 + H -3.64797 -0.34668 -4.58854 + H -3.54956 0.03463 -2.88617 +16 + Configuration number : 50000L = 26.5871 26.5871 26.5871 + C 0.32518 -0.85356 -4.42677 + C -1.07260 -0.83972 -4.34908 + C -1.73632 0.31774 -3.95111 + C -1.00588 1.46773 -3.62865 + C 0.38424 1.45396 -3.70592 + C 1.05167 0.29018 -4.10605 + H 0.84000 -1.75140 -4.73541 + H -1.63609 -1.72684 -4.59780 + H -1.52068 2.36557 -3.31999 + H 2.12995 0.27949 -4.16599 + O 1.09379 2.57109 -3.39267 + H 0.48991 3.27346 -3.14064 + C -3.24394 0.33266 -3.86731 + H -3.60250 1.32066 -4.06784 + H -3.64798 -0.34664 -4.58853 + H -3.54958 0.03461 -2.88619 +16 + Configuration number : 50000L = 26.5871 26.5871 26.5871 + C 0.32514 -0.85357 -4.42672 + C -1.07259 -0.83971 -4.34908 + C -1.73630 0.31776 -3.95111 + C -1.00590 1.46773 -3.62865 + C 0.38424 1.45397 -3.70593 + C 1.05165 0.29017 -4.10605 + H 0.84000 -1.75143 -4.73546 + H -1.63610 -1.72693 -4.59783 + H -1.52069 2.36557 -3.32000 + H 2.12993 0.27951 -4.16597 + O 1.09379 2.57106 -3.39268 + H 0.48990 3.27351 -3.14063 + C -3.24389 0.33268 -3.86730 + H -3.60246 1.32066 -4.06782 + H -3.64795 -0.34665 -4.58855 + H -3.54950 0.03463 -2.88621 +16 + Configuration number : 50000L = 26.5871 26.5871 26.5871 + C 0.32518 -0.85360 -4.42675 + C -1.07258 -0.83974 -4.34906 + C -1.73633 0.31774 -3.95111 + C -1.00589 1.46774 -3.62865 + C 0.38425 1.45398 -3.70591 + C 1.05167 0.29018 -4.10606 + H 0.83997 -1.75139 -4.73541 + H -1.63608 -1.72682 -4.59780 + H -1.52070 2.36555 -3.31996 + H 2.12995 0.27951 -4.16596 + O 1.09382 2.57111 -3.39268 + H 0.48993 3.27344 -3.14064 + C -3.24396 0.33265 -3.86732 + H -3.60255 1.32066 -4.06785 + H -3.64801 -0.34665 -4.58854 + H -3.54959 0.03460 -2.88619 +16 + Configuration number : 50000L = 26.5871 26.5871 26.5871 + C 0.32516 -0.85360 -4.42674 + C -1.07258 -0.83972 -4.34905 + C -1.73632 0.31774 -3.95111 + C -1.00590 1.46773 -3.62865 + C 0.38423 1.45396 -3.70593 + C 1.05168 0.29015 -4.10603 + H 0.83997 -1.75146 -4.73545 + H -1.63604 -1.72685 -4.59781 + H -1.52071 2.36557 -3.31996 + H 2.12993 0.27949 -4.16598 + O 1.09379 2.57111 -3.39269 + H 0.48987 3.27345 -3.14062 + C -3.24389 0.33269 -3.86733 + H -3.60250 1.32066 -4.06785 + H -3.64801 -0.34665 -4.58854 + H -3.54958 0.03460 -2.88617 +16 + Configuration number : 50000L = 26.5871 26.5871 26.5871 + C 0.32520 -0.85359 -4.42675 + C -1.07259 -0.83973 -4.34906 + C -1.73634 0.31772 -3.95110 + C -1.00591 1.46774 -3.62867 + C 0.38424 1.45396 -3.70593 + C 1.05171 0.29015 -4.10606 + H 0.83997 -1.75136 -4.73543 + H -1.63607 -1.72684 -4.59779 + H -1.52071 2.36559 -3.31995 + H 2.12995 0.27946 -4.16598 + O 1.09381 2.57111 -3.39267 + H 0.48988 3.27350 -3.14063 + C -3.24396 0.33270 -3.86732 + H -3.60254 1.32067 -4.06784 + H -3.64801 -0.34663 -4.58854 + H -3.54961 0.03458 -2.88619 +16 + Configuration number : 50000L = 26.5871 26.5871 26.5871 + C 0.32520 -0.85358 -4.42675 + C -1.07259 -0.83974 -4.34907 + C -1.73634 0.31774 -3.95110 + C -1.00591 1.46776 -3.62865 + C 0.38424 1.45395 -3.70592 + C 1.05168 0.29017 -4.10606 + H 0.83999 -1.75144 -4.73543 + H -1.63608 -1.72686 -4.59780 + H -1.52072 2.36558 -3.31996 + H 2.13001 0.27950 -4.16599 + O 1.09380 2.57109 -3.39267 + H 0.48988 3.27348 -3.14063 + C -3.24393 0.33268 -3.86732 + H -3.60258 1.32070 -4.06785 + H -3.64800 -0.34664 -4.58856 + H -3.54963 0.03459 -2.88614 +16 + Configuration number : 50000L = 26.5871 26.5871 26.5871 + C 0.32519 -0.85360 -4.42676 + C -1.07258 -0.83972 -4.34907 + C -1.73632 0.31774 -3.95110 + C -1.00589 1.46775 -3.62865 + C 0.38423 1.45395 -3.70592 + C 1.05164 0.29016 -4.10603 + H 0.83998 -1.75140 -4.73545 + H -1.63607 -1.72686 -4.59781 + H -1.52069 2.36556 -3.31997 + H 2.12994 0.27949 -4.16599 + O 1.09377 2.57111 -3.39268 + H 0.48989 3.27344 -3.14064 + C -3.24388 0.33268 -3.86732 + H -3.60249 1.32069 -4.06789 + H -3.64792 -0.34664 -4.58852 + H -3.54957 0.03461 -2.88615 +16 + Configuration number : 50000L = 26.5871 26.5871 26.5871 + C 0.32517 -0.85358 -4.42676 + C -1.07258 -0.83971 -4.34906 + C -1.73633 0.31774 -3.95110 + C -1.00588 1.46775 -3.62865 + C 0.38424 1.45396 -3.70591 + C 1.05165 0.29014 -4.10604 + H 0.84000 -1.75142 -4.73544 + H -1.63608 -1.72685 -4.59779 + H -1.52070 2.36556 -3.31997 + H 2.12992 0.27951 -4.16595 + O 1.09380 2.57109 -3.39269 + H 0.48989 3.27349 -3.14062 + C -3.24392 0.33269 -3.86733 + H -3.60250 1.32065 -4.06782 + H -3.64795 -0.34663 -4.58853 + H -3.54960 0.03460 -2.88618 +16 + Configuration number : 50000L = 26.5871 26.5871 26.5871 + C 0.32519 -0.85356 -4.42675 + C -1.07258 -0.83971 -4.34905 + C -1.73632 0.31775 -3.95112 + C -1.00589 1.46774 -3.62866 + C 0.38420 1.45394 -3.70592 + C 1.05163 0.29015 -4.10605 + H 0.84000 -1.75139 -4.73543 + H -1.63605 -1.72683 -4.59780 + H -1.52069 2.36557 -3.31997 + H 2.12997 0.27951 -4.16597 + O 1.09380 2.57108 -3.39268 + H 0.48988 3.27346 -3.14064 + C -3.24390 0.33268 -3.86732 + H -3.60248 1.32068 -4.06784 + H -3.64792 -0.34661 -4.58853 + H -3.54955 0.03461 -2.88617 +16 + Configuration number : 50000L = 26.5871 26.5871 26.5871 + C 0.32520 -0.85358 -4.42677 + C -1.07258 -0.83973 -4.34907 + C -1.73632 0.31773 -3.95110 + C -1.00591 1.46775 -3.62865 + C 0.38422 1.45396 -3.70592 + C 1.05167 0.29016 -4.10606 + H 0.83996 -1.75137 -4.73543 + H -1.63605 -1.72683 -4.59778 + H -1.52072 2.36555 -3.31998 + H 2.12993 0.27947 -4.16598 + O 1.09380 2.57109 -3.39266 + H 0.48990 3.27350 -3.14063 + C -3.24393 0.33269 -3.86732 + H -3.60251 1.32068 -4.06787 + H -3.64798 -0.34665 -4.58853 + H -3.54957 0.03461 -2.88617 +16 + Configuration number : 50000L = 26.5871 26.5871 26.5871 + C 0.32520 -0.85359 -4.42675 + C -1.07259 -0.83974 -4.34906 + C -1.73632 0.31775 -3.95111 + C -1.00589 1.46775 -3.62864 + C 0.38424 1.45397 -3.70593 + C 1.05164 0.29016 -4.10605 + H 0.84000 -1.75139 -4.73544 + H -1.63608 -1.72686 -4.59780 + H -1.52071 2.36558 -3.31998 + H 2.12991 0.27950 -4.16600 + O 1.09380 2.57111 -3.39267 + H 0.48989 3.27346 -3.14063 + C -3.24393 0.33266 -3.86732 + H -3.60251 1.32069 -4.06785 + H -3.64796 -0.34664 -4.58855 + H -3.54955 0.03463 -2.88617 +16 + Configuration number : 50000L = 26.5871 26.5871 26.5871 + C 0.32518 -0.85357 -4.42676 + C -1.07260 -0.83974 -4.34906 + C -1.73632 0.31774 -3.95111 + C -1.00590 1.46774 -3.62866 + C 0.38423 1.45397 -3.70591 + C 1.05167 0.29017 -4.10605 + H 0.84000 -1.75140 -4.73542 + H -1.63607 -1.72682 -4.59782 + H -1.52070 2.36558 -3.31997 + H 2.12995 0.27948 -4.16597 + O 1.09378 2.57108 -3.39268 + H 0.48989 3.27350 -3.14063 + C -3.24389 0.33269 -3.86732 + H -3.60254 1.32067 -4.06784 + H -3.64794 -0.34661 -4.58852 + H -3.54959 0.03460 -2.88617 +16 + Configuration number : 50000L = 26.5871 26.5871 26.5871 + C 0.32518 -0.85358 -4.42675 + C -1.07260 -0.83973 -4.34907 + C -1.73632 0.31775 -3.95112 + C -1.00589 1.46775 -3.62865 + C 0.38424 1.45395 -3.70592 + C 1.05165 0.29016 -4.10605 + H 0.84001 -1.75143 -4.73543 + H -1.63608 -1.72684 -4.59779 + H -1.52069 2.36555 -3.31995 + H 2.12996 0.27947 -4.16597 + O 1.09378 2.57108 -3.39267 + H 0.48990 3.27351 -3.14061 + C -3.24389 0.33271 -3.86733 + H -3.60252 1.32066 -4.06783 + H -3.64798 -0.34668 -4.58853 + H -3.54960 0.03459 -2.88616 +16 + Configuration number : 50000L = 26.5871 26.5871 26.5871 + C 0.32518 -0.85359 -4.42674 + C -1.07260 -0.83972 -4.34906 + C -1.73632 0.31775 -3.95111 + C -1.00590 1.46774 -3.62864 + C 0.38424 1.45395 -3.70593 + C 1.05166 0.29017 -4.10605 + H 0.83999 -1.75135 -4.73547 + H -1.63608 -1.72687 -4.59780 + H -1.52072 2.36558 -3.31997 + H 2.12992 0.27948 -4.16596 + O 1.09379 2.57108 -3.39269 + H 0.48988 3.27345 -3.14066 + C -3.24389 0.33270 -3.86731 + H -3.60252 1.32065 -4.06786 + H -3.64799 -0.34664 -4.58854 + H -3.54959 0.03461 -2.88617 +16 + Configuration number : 50000L = 26.5871 26.5871 26.5871 + C 0.32518 -0.85358 -4.42675 + C -1.07259 -0.83973 -4.34907 + C -1.73631 0.31775 -3.95111 + C -1.00590 1.46773 -3.62866 + C 0.38423 1.45395 -3.70591 + C 1.05167 0.29016 -4.10604 + H 0.83998 -1.75139 -4.73543 + H -1.63608 -1.72685 -4.59781 + H -1.52070 2.36556 -3.31997 + H 2.12993 0.27949 -4.16599 + O 1.09378 2.57109 -3.39269 + H 0.48987 3.27348 -3.14063 + C -3.24391 0.33270 -3.86733 + H -3.60249 1.32064 -4.06785 + H -3.64793 -0.34661 -4.58853 + H -3.54954 0.03464 -2.88616 +16 + Configuration number : 50000L = 26.5871 26.5871 26.5871 + C 0.32518 -0.85356 -4.42675 + C -1.07259 -0.83973 -4.34907 + C -1.73632 0.31775 -3.95111 + C -1.00588 1.46775 -3.62865 + C 0.38423 1.45396 -3.70590 + C 1.05165 0.29016 -4.10604 + H 0.84000 -1.75140 -4.73544 + H -1.63607 -1.72687 -4.59780 + H -1.52068 2.36555 -3.31999 + H 2.12996 0.27949 -4.16597 + O 1.09381 2.57108 -3.39269 + H 0.48989 3.27349 -3.14062 + C -3.24394 0.33267 -3.86734 + H -3.60253 1.32068 -4.06784 + H -3.64797 -0.34662 -4.58854 + H -3.54954 0.03460 -2.88617 +16 + Configuration number : 50000L = 26.5871 26.5871 26.5871 + C 0.32518 -0.85356 -4.42673 + C -1.07261 -0.83970 -4.34906 + C -1.73632 0.31775 -3.95111 + C -1.00589 1.46772 -3.62866 + C 0.38423 1.45395 -3.70592 + C 1.05167 0.29016 -4.10606 + H 0.83999 -1.75138 -4.73543 + H -1.63605 -1.72684 -4.59782 + H -1.52074 2.36557 -3.31997 + H 2.12994 0.27947 -4.16597 + O 1.09380 2.57108 -3.39268 + H 0.48991 3.27344 -3.14066 + C -3.24391 0.33269 -3.86731 + H -3.60252 1.32067 -4.06784 + H -3.64800 -0.34666 -4.58851 + H -3.54957 0.03460 -2.88620 +16 + Configuration number : 50000L = 26.5871 26.5871 26.5871 + C 0.32519 -0.85360 -4.42675 + C -1.07258 -0.83973 -4.34907 + C -1.73632 0.31776 -3.95111 + C -1.00591 1.46775 -3.62864 + C 0.38422 1.45396 -3.70591 + C 1.05166 0.29016 -4.10604 + H 0.84000 -1.75142 -4.73542 + H -1.63607 -1.72689 -4.59782 + H -1.52072 2.36559 -3.31995 + H 2.12996 0.27949 -4.16600 + O 1.09379 2.57108 -3.39269 + H 0.48990 3.27351 -3.14062 + C -3.24391 0.33269 -3.86733 + H -3.60249 1.32067 -4.06781 + H -3.64796 -0.34662 -4.58855 + H -3.54954 0.03462 -2.88619 +16 + Configuration number : 50000L = 26.5871 26.5871 26.5871 + C 0.32518 -0.85358 -4.42676 + C -1.07260 -0.83975 -4.34907 + C -1.73629 0.31776 -3.95111 + C -1.00589 1.46776 -3.62865 + C 0.38424 1.45395 -3.70591 + C 1.05165 0.29019 -4.10605 + H 0.84001 -1.75141 -4.73546 + H -1.63606 -1.72683 -4.59779 + H -1.52070 2.36558 -3.31998 + H 2.12995 0.27948 -4.16598 + O 1.09379 2.57106 -3.39267 + H 0.48988 3.27349 -3.14064 + C -3.24391 0.33269 -3.86732 + H -3.60254 1.32066 -4.06786 + H -3.64795 -0.34663 -4.58853 + H -3.54959 0.03462 -2.88615 +16 + Configuration number : 50000L = 26.5871 26.5871 26.5871 + C 0.32519 -0.85357 -4.42676 + C -1.07259 -0.83972 -4.34907 + C -1.73633 0.31775 -3.95110 + C -1.00590 1.46773 -3.62866 + C 0.38421 1.45394 -3.70593 + C 1.05166 0.29016 -4.10605 + H 0.83998 -1.75136 -4.73541 + H -1.63606 -1.72687 -4.59782 + H -1.52072 2.36555 -3.31996 + H 2.12996 0.27948 -4.16599 + O 1.09381 2.57109 -3.39268 + H 0.48987 3.27346 -3.14065 + C -3.24390 0.33269 -3.86730 + H -3.60251 1.32067 -4.06785 + H -3.64797 -0.34662 -4.58852 + H -3.54962 0.03460 -2.88619 +16 + Configuration number : 50000L = 26.5871 26.5871 26.5871 + C 0.32520 -0.85358 -4.42676 + C -1.07258 -0.83972 -4.34906 + C -1.73633 0.31775 -3.95112 + C -1.00591 1.46774 -3.62865 + C 0.38425 1.45398 -3.70592 + C 1.05168 0.29018 -4.10606 + H 0.84000 -1.75139 -4.73545 + H -1.63607 -1.72690 -4.59782 + H -1.52071 2.36558 -3.31997 + H 2.13003 0.27946 -4.16597 + O 1.09381 2.57107 -3.39267 + H 0.48989 3.27354 -3.14064 + C -3.24397 0.33267 -3.86730 + H -3.60253 1.32068 -4.06787 + H -3.64802 -0.34662 -4.58852 + H -3.54959 0.03462 -2.88618 +16 + Configuration number : 50000L = 26.5871 26.5871 26.5871 + C 0.32518 -0.85357 -4.42676 + C -1.07260 -0.83970 -4.34905 + C -1.73632 0.31774 -3.95111 + C -1.00589 1.46773 -3.62865 + C 0.38422 1.45396 -3.70592 + C 1.05167 0.29016 -4.10607 + H 0.84000 -1.75137 -4.73542 + H -1.63606 -1.72683 -4.59779 + H -1.52070 2.36557 -3.31996 + H 2.12991 0.27950 -4.16595 + O 1.09378 2.57108 -3.39269 + H 0.48989 3.27346 -3.14061 + C -3.24389 0.33268 -3.86730 + H -3.60248 1.32069 -4.06785 + H -3.64795 -0.34664 -4.58855 + H -3.54957 0.03462 -2.88617 +16 + Configuration number : 50000L = 26.5871 26.5871 26.5871 + C 0.32518 -0.85361 -4.42676 + C -1.07260 -0.83974 -4.34907 + C -1.73632 0.31774 -3.95111 + C -1.00590 1.46776 -3.62865 + C 0.38423 1.45396 -3.70591 + C 1.05169 0.29015 -4.10605 + H 0.83997 -1.75139 -4.73543 + H -1.63608 -1.72685 -4.59781 + H -1.52072 2.36559 -3.31997 + H 2.12995 0.27947 -4.16599 + O 1.09381 2.57113 -3.39267 + H 0.48990 3.27350 -3.14063 + C -3.24393 0.33267 -3.86732 + H -3.60249 1.32064 -4.06784 + H -3.64796 -0.34664 -4.58854 + H -3.54960 0.03462 -2.88617 +16 + Configuration number : 50000L = 26.5871 26.5871 26.5871 + C 0.32519 -0.85357 -4.42675 + C -1.07259 -0.83973 -4.34906 + C -1.73633 0.31774 -3.95112 + C -1.00591 1.46775 -3.62865 + C 0.38422 1.45396 -3.70592 + C 1.05169 0.29015 -4.10605 + H 0.84001 -1.75138 -4.73544 + H -1.63605 -1.72685 -4.59779 + H -1.52073 2.36558 -3.31998 + H 2.12994 0.27949 -4.16599 + O 1.09380 2.57107 -3.39266 + H 0.48988 3.27350 -3.14063 + C -3.24393 0.33270 -3.86733 + H -3.60251 1.32068 -4.06784 + H -3.64797 -0.34661 -4.58853 + H -3.54957 0.03462 -2.88616 +16 + Configuration number : 50000L = 26.5871 26.5871 26.5871 + C 0.32516 -0.85357 -4.42676 + C -1.07260 -0.83971 -4.34906 + C -1.73632 0.31776 -3.95110 + C -1.00591 1.46773 -3.62865 + C 0.38423 1.45395 -3.70592 + C 1.05166 0.29016 -4.10605 + H 0.83998 -1.75137 -4.73544 + H -1.63605 -1.72684 -4.59780 + H -1.52071 2.36553 -3.31997 + H 2.12994 0.27951 -4.16597 + O 1.09380 2.57107 -3.39268 + H 0.48990 3.27348 -3.14064 + C -3.24389 0.33269 -3.86733 + H -3.60249 1.32065 -4.06785 + H -3.64794 -0.34663 -4.58848 + H -3.54960 0.03463 -2.88622 +16 + Configuration number : 50000L = 26.5871 26.5871 26.5871 + C 0.32519 -0.85358 -4.42674 + C -1.07260 -0.83970 -4.34906 + C -1.73631 0.31776 -3.95111 + C -1.00590 1.46773 -3.62865 + C 0.38421 1.45395 -3.70591 + C 1.05165 0.29016 -4.10606 + H 0.83995 -1.75136 -4.73541 + H -1.63606 -1.72683 -4.59780 + H -1.52070 2.36555 -3.31997 + H 2.12992 0.27949 -4.16595 + O 1.09380 2.57108 -3.39269 + H 0.48990 3.27345 -3.14063 + C -3.24389 0.33268 -3.86732 + H -3.60248 1.32065 -4.06783 + H -3.64794 -0.34662 -4.58853 + H -3.54958 0.03460 -2.88617 +16 + Configuration number : 50000L = 26.5871 26.5871 26.5871 + C 0.32517 -0.85359 -4.42675 + C -1.07259 -0.83975 -4.34906 + C -1.73634 0.31773 -3.95110 + C -1.00590 1.46774 -3.62864 + C 0.38425 1.45397 -3.70592 + C 1.05166 0.29017 -4.10604 + H 0.84003 -1.75143 -4.73545 + H -1.63606 -1.72685 -4.59781 + H -1.52070 2.36557 -3.31996 + H 2.12998 0.27948 -4.16597 + O 1.09382 2.57112 -3.39267 + H 0.48990 3.27351 -3.14063 + C -3.24394 0.33268 -3.86734 + H -3.60250 1.32069 -4.06784 + H -3.64795 -0.34663 -4.58851 + H -3.54954 0.03462 -2.88620 +16 + Configuration number : 50000L = 26.5871 26.5871 26.5871 + C 0.32518 -0.85357 -4.42675 + C -1.07260 -0.83974 -4.34907 + C -1.73631 0.31776 -3.95109 + C -1.00589 1.46776 -3.62865 + C 0.38424 1.45396 -3.70593 + C 1.05168 0.29016 -4.10605 + H 0.83998 -1.75136 -4.73542 + H -1.63607 -1.72688 -4.59782 + H -1.52070 2.36558 -3.31997 + H 2.12997 0.27950 -4.16598 + O 1.09377 2.57107 -3.39268 + H 0.48992 3.27351 -3.14062 + C -3.24392 0.33269 -3.86733 + H -3.60249 1.32066 -4.06784 + H -3.64798 -0.34665 -4.58854 + H -3.54956 0.03462 -2.88617 +16 + Configuration number : 50000L = 26.5871 26.5871 26.5871 + C 0.32517 -0.85356 -4.42676 + C -1.07261 -0.83973 -4.34906 + C -1.73633 0.31774 -3.95112 + C -1.00589 1.46774 -3.62866 + C 0.38424 1.45397 -3.70592 + C 1.05167 0.29017 -4.10605 + H 0.83996 -1.75136 -4.73542 + H -1.63610 -1.72688 -4.59781 + H -1.52070 2.36558 -3.31998 + H 2.12990 0.27950 -4.16598 + O 1.09382 2.57106 -3.39269 + H 0.48987 3.27352 -3.14062 + C -3.24391 0.33268 -3.86729 + H -3.60251 1.32065 -4.06783 + H -3.64800 -0.34666 -4.58856 + H -3.54961 0.03461 -2.88620 +16 + Configuration number : 50000L = 26.5871 26.5871 26.5871 + C 0.32517 -0.85356 -4.42674 + C -1.07259 -0.83972 -4.34906 + C -1.73629 0.31776 -3.95111 + C -1.00590 1.46774 -3.62865 + C 0.38423 1.45394 -3.70592 + C 1.05164 0.29016 -4.10606 + H 0.83999 -1.75139 -4.73545 + H -1.63606 -1.72685 -4.59781 + H -1.52071 2.36554 -3.31998 + H 2.12997 0.27945 -4.16598 + O 1.09379 2.57108 -3.39268 + H 0.48989 3.27347 -3.14063 + C -3.24391 0.33268 -3.86732 + H -3.60247 1.32065 -4.06786 + H -3.64798 -0.34666 -4.58855 + H -3.54952 0.03464 -2.88617 +16 + Configuration number : 50000L = 26.5871 26.5871 26.5871 + C 0.32518 -0.85357 -4.42675 + C -1.07258 -0.83974 -4.34907 + C -1.73630 0.31775 -3.95110 + C -1.00590 1.46775 -3.62866 + C 0.38422 1.45394 -3.70592 + C 1.05167 0.29017 -4.10603 + H 0.84000 -1.75142 -4.73544 + H -1.63607 -1.72685 -4.59782 + H -1.52070 2.36556 -3.31997 + H 2.12994 0.27950 -4.16598 + O 1.09379 2.57108 -3.39269 + H 0.48988 3.27348 -3.14064 + C -3.24392 0.33268 -3.86730 + H -3.60247 1.32068 -4.06784 + H -3.64798 -0.34663 -4.58855 + H -3.54956 0.03462 -2.88618 +16 + Configuration number : 50000L = 26.5871 26.5871 26.5871 + C 0.32519 -0.85357 -4.42677 + C -1.07259 -0.83971 -4.34906 + C -1.73633 0.31775 -3.95111 + C -1.00589 1.46773 -3.62866 + C 0.38423 1.45396 -3.70592 + C 1.05169 0.29016 -4.10603 + H 0.83999 -1.75134 -4.73544 + H -1.63606 -1.72687 -4.59780 + H -1.52068 2.36555 -3.31999 + H 2.12991 0.27949 -4.16598 + O 1.09380 2.57108 -3.39268 + H 0.48991 3.27346 -3.14064 + C -3.24393 0.33268 -3.86731 + H -3.60249 1.32066 -4.06786 + H -3.64797 -0.34664 -4.58853 + H -3.54959 0.03463 -2.88617 +16 + Configuration number : 50000L = 26.5871 26.5871 26.5871 + C 0.32516 -0.85359 -4.42675 + C -1.07259 -0.83972 -4.34907 + C -1.73630 0.31775 -3.95109 + C -1.00590 1.46774 -3.62866 + C 0.38422 1.45395 -3.70591 + C 1.05166 0.29017 -4.10604 + H 0.83998 -1.75143 -4.73544 + H -1.63607 -1.72686 -4.59783 + H -1.52071 2.36554 -3.31998 + H 2.12994 0.27947 -4.16598 + O 1.09378 2.57109 -3.39268 + H 0.48987 3.27346 -3.14064 + C -3.24388 0.33270 -3.86733 + H -3.60249 1.32066 -4.06784 + H -3.64794 -0.34664 -4.58853 + H -3.54957 0.03461 -2.88616 +16 + Configuration number : 50000L = 26.5871 26.5871 26.5871 + C 0.32518 -0.85357 -4.42674 + C -1.07258 -0.83972 -4.34907 + C -1.73633 0.31775 -3.95111 + C -1.00589 1.46774 -3.62865 + C 0.38422 1.45395 -3.70591 + C 1.05167 0.29016 -4.10606 + H 0.83999 -1.75138 -4.73540 + H -1.63606 -1.72683 -4.59782 + H -1.52070 2.36557 -3.31996 + H 2.12997 0.27947 -4.16601 + O 1.09377 2.57108 -3.39267 + H 0.48989 3.27349 -3.14065 + C -3.24388 0.33269 -3.86733 + H -3.60251 1.32067 -4.06786 + H -3.64800 -0.34662 -4.58853 + H -3.54959 0.03458 -2.88617 +16 + Configuration number : 50000L = 26.5871 26.5871 26.5871 + C 0.32521 -0.85360 -4.42676 + C -1.07259 -0.83971 -4.34905 + C -1.73632 0.31774 -3.95110 + C -1.00589 1.46774 -3.62865 + C 0.38424 1.45398 -3.70592 + C 1.05165 0.29016 -4.10604 + H 0.83997 -1.75140 -4.73543 + H -1.63607 -1.72688 -4.59782 + H -1.52072 2.36556 -3.31997 + H 2.12994 0.27948 -4.16597 + O 1.09377 2.57108 -3.39269 + H 0.48991 3.27352 -3.14061 + C -3.24391 0.33269 -3.86733 + H -3.60255 1.32069 -4.06786 + H -3.64798 -0.34664 -4.58854 + H -3.54952 0.03462 -2.88616 +16 + Configuration number : 50000L = 26.5871 26.5871 26.5871 + C 0.32518 -0.85358 -4.42677 + C -1.07258 -0.83971 -4.34906 + C -1.73632 0.31774 -3.95110 + C -1.00589 1.46773 -3.62865 + C 0.38423 1.45396 -3.70593 + C 1.05166 0.29016 -4.10605 + H 0.83998 -1.75141 -4.73546 + H -1.63604 -1.72682 -4.59780 + H -1.52070 2.36560 -3.31995 + H 2.12995 0.27948 -4.16594 + O 1.09380 2.57108 -3.39267 + H 0.48987 3.27348 -3.14066 + C -3.24394 0.33268 -3.86731 + H -3.60252 1.32068 -4.06787 + H -3.64790 -0.34662 -4.58852 + H -3.54954 0.03461 -2.88616 +16 + Configuration number : 50000L = 26.5871 26.5871 26.5871 + C 0.32516 -0.85356 -4.42674 + C -1.07259 -0.83972 -4.34906 + C -1.73632 0.31776 -3.95110 + C -1.00589 1.46772 -3.62866 + C 0.38421 1.45394 -3.70593 + C 1.05166 0.29016 -4.10605 + H 0.83997 -1.75139 -4.73543 + H -1.63607 -1.72686 -4.59783 + H -1.52072 2.36557 -3.31998 + H 2.12989 0.27948 -4.16598 + O 1.09380 2.57109 -3.39267 + H 0.48988 3.27347 -3.14065 + C -3.24389 0.33268 -3.86733 + H -3.60249 1.32065 -4.06783 + H -3.64796 -0.34664 -4.58852 + H -3.54954 0.03463 -2.88620 +16 + Configuration number : 50000L = 26.5871 26.5871 26.5871 + C 0.32519 -0.85360 -4.42675 + C -1.07261 -0.83973 -4.34906 + C -1.73634 0.31773 -3.95112 + C -1.00589 1.46775 -3.62864 + C 0.38424 1.45396 -3.70592 + C 1.05168 0.29018 -4.10604 + H 0.84000 -1.75141 -4.73542 + H -1.63609 -1.72686 -4.59782 + H -1.52069 2.36560 -3.31996 + H 2.12995 0.27947 -4.16600 + O 1.09378 2.57109 -3.39269 + H 0.48987 3.27346 -3.14063 + C -3.24389 0.33268 -3.86730 + H -3.60255 1.32068 -4.06785 + H -3.64799 -0.34664 -4.58855 + H -3.54956 0.03460 -2.88619 +16 + Configuration number : 50000L = 26.5871 26.5871 26.5871 + C 0.32518 -0.85357 -4.42675 + C -1.07260 -0.83973 -4.34906 + C -1.73631 0.31776 -3.95111 + C -1.00589 1.46774 -3.62865 + C 0.38425 1.45395 -3.70591 + C 1.05165 0.29016 -4.10604 + H 0.84002 -1.75139 -4.73542 + H -1.63607 -1.72686 -4.59780 + H -1.52071 2.36555 -3.31995 + H 2.12995 0.27950 -4.16599 + O 1.09378 2.57107 -3.39269 + H 0.48990 3.27349 -3.14063 + C -3.24391 0.33269 -3.86732 + H -3.60252 1.32070 -4.06784 + H -3.64796 -0.34664 -4.58854 + H -3.54953 0.03462 -2.88618 +16 + Configuration number : 50000L = 26.5871 26.5871 26.5871 + C 0.32518 -0.85358 -4.42674 + C -1.07259 -0.83971 -4.34906 + C -1.73631 0.31774 -3.95110 + C -1.00592 1.46775 -3.62866 + C 0.38424 1.45395 -3.70591 + C 1.05167 0.29017 -4.10607 + H 0.83998 -1.75137 -4.73541 + H -1.63608 -1.72687 -4.59781 + H -1.52072 2.36556 -3.31996 + H 2.12993 0.27949 -4.16598 + O 1.09380 2.57107 -3.39269 + H 0.48989 3.27349 -3.14062 + C -3.24391 0.33268 -3.86730 + H -3.60248 1.32067 -4.06784 + H -3.64795 -0.34663 -4.58854 + H -3.54958 0.03462 -2.88618 +16 + Configuration number : 50000L = 26.5871 26.5871 26.5871 + C 0.32519 -0.85357 -4.42676 + C -1.07259 -0.83972 -4.34907 + C -1.73632 0.31776 -3.95110 + C -1.00590 1.46773 -3.62864 + C 0.38422 1.45393 -3.70592 + C 1.05166 0.29016 -4.10605 + H 0.83999 -1.75136 -4.73543 + H -1.63605 -1.72685 -4.59780 + H -1.52072 2.36555 -3.31996 + H 2.12995 0.27947 -4.16596 + O 1.09379 2.57108 -3.39269 + H 0.48988 3.27349 -3.14064 + C -3.24389 0.33270 -3.86730 + H -3.60253 1.32069 -4.06785 + H -3.64795 -0.34664 -4.58851 + H -3.54954 0.03464 -2.88621 +16 + Configuration number : 50000L = 26.5871 26.5871 26.5871 + C 0.32517 -0.85356 -4.42674 + C -1.07260 -0.83973 -4.34907 + C -1.73634 0.31774 -3.95111 + C -1.00589 1.46774 -3.62865 + C 0.38427 1.45397 -3.70591 + C 1.05167 0.29017 -4.10606 + H 0.83994 -1.75136 -4.73544 + H -1.63604 -1.72684 -4.59780 + H -1.52069 2.36557 -3.31997 + H 2.12997 0.27949 -4.16600 + O 1.09382 2.57108 -3.39267 + H 0.48991 3.27349 -3.14065 + C -3.24395 0.33265 -3.86732 + H -3.60253 1.32068 -4.06788 + H -3.64792 -0.34667 -4.58855 + H -3.54952 0.03463 -2.88617 +16 + Configuration number : 50000L = 26.5871 26.5871 26.5871 + C 0.32517 -0.85357 -4.42672 + C -1.07259 -0.83969 -4.34904 + C -1.73632 0.31773 -3.95110 + C -1.00590 1.46772 -3.62866 + C 0.38422 1.45395 -3.70593 + C 1.05167 0.29018 -4.10606 + H 0.83998 -1.75140 -4.73544 + H -1.63609 -1.72687 -4.59782 + H -1.52072 2.36554 -3.31998 + H 2.12992 0.27951 -4.16598 + O 1.09379 2.57107 -3.39269 + H 0.48988 3.27346 -3.14065 + C -3.24389 0.33267 -3.86731 + H -3.60249 1.32067 -4.06784 + H -3.64795 -0.34660 -4.58855 + H -3.54954 0.03462 -2.88620 +16 + Configuration number : 50000L = 26.5871 26.5871 26.5871 + C 0.32520 -0.85359 -4.42676 + C -1.07259 -0.83972 -4.34906 + C -1.73635 0.31775 -3.95111 + C -1.00590 1.46775 -3.62865 + C 0.38423 1.45396 -3.70592 + C 1.05168 0.29016 -4.10603 + H 0.83997 -1.75141 -4.73542 + H -1.63608 -1.72684 -4.59781 + H -1.52070 2.36556 -3.31994 + H 2.12993 0.27948 -4.16598 + O 1.09379 2.57109 -3.39268 + H 0.48989 3.27351 -3.14064 + C -3.24390 0.33267 -3.86732 + H -3.60253 1.32067 -4.06784 + H -3.64801 -0.34666 -4.58855 + H -3.54958 0.03462 -2.88617 +16 + Configuration number : 50000L = 26.5871 26.5871 26.5871 + C 0.32518 -0.85356 -4.42676 + C -1.07260 -0.83972 -4.34907 + C -1.73634 0.31774 -3.95111 + C -1.00590 1.46774 -3.62865 + C 0.38424 1.45398 -3.70592 + C 1.05166 0.29015 -4.10605 + H 0.84000 -1.75139 -4.73540 + H -1.63609 -1.72683 -4.59782 + H -1.52070 2.36556 -3.31998 + H 2.12992 0.27951 -4.16598 + O 1.09384 2.57109 -3.39266 + H 0.48992 3.27351 -3.14064 + C -3.24393 0.33265 -3.86733 + H -3.60249 1.32067 -4.06784 + H -3.64797 -0.34665 -4.58850 + H -3.54958 0.03462 -2.88619 +16 + Configuration number : 50000L = 26.5871 26.5871 26.5871 + C 0.32517 -0.85358 -4.42674 + C -1.07258 -0.83971 -4.34905 + C -1.73632 0.31774 -3.95111 + C -1.00590 1.46773 -3.62866 + C 0.38423 1.45394 -3.70592 + C 1.05166 0.29017 -4.10605 + H 0.83994 -1.75133 -4.73542 + H -1.63608 -1.72684 -4.59783 + H -1.52072 2.36555 -3.31996 + H 2.12993 0.27948 -4.16600 + O 1.09380 2.57109 -3.39270 + H 0.48985 3.27348 -3.14064 + C -3.24388 0.33269 -3.86730 + H -3.60251 1.32066 -4.06786 + H -3.64798 -0.34663 -4.58854 + H -3.54966 0.03461 -2.88618 +16 + Configuration number : 50000L = 26.5871 26.5871 26.5871 + C 0.32517 -0.85359 -4.42674 + C -1.07259 -0.83973 -4.34905 + C -1.73631 0.31774 -3.95111 + C -1.00588 1.46773 -3.62866 + C 0.38423 1.45396 -3.70592 + C 1.05165 0.29016 -4.10607 + H 0.83996 -1.75140 -4.73546 + H -1.63607 -1.72688 -4.59781 + H -1.52069 2.36556 -3.31999 + H 2.12991 0.27949 -4.16600 + O 1.09380 2.57112 -3.39268 + H 0.48988 3.27349 -3.14064 + C -3.24391 0.33268 -3.86731 + H -3.60250 1.32069 -4.06786 + H -3.64795 -0.34665 -4.58856 + H -3.54957 0.03461 -2.88620 +16 + Configuration number : 50000L = 26.5871 26.5871 26.5871 + C 0.32517 -0.85356 -4.42676 + C -1.07259 -0.83973 -4.34905 + C -1.73632 0.31774 -3.95111 + C -1.00590 1.46775 -3.62866 + C 0.38424 1.45396 -3.70592 + C 1.05166 0.29017 -4.10605 + H 0.84001 -1.75142 -4.73544 + H -1.63606 -1.72684 -4.59781 + H -1.52069 2.36556 -3.31996 + H 2.12993 0.27946 -4.16597 + O 1.09380 2.57107 -3.39267 + H 0.48988 3.27347 -3.14064 + C -3.24391 0.33268 -3.86732 + H -3.60250 1.32066 -4.06784 + H -3.64794 -0.34663 -4.58852 + H -3.54957 0.03461 -2.88618 +16 + Configuration number : 50000L = 26.5871 26.5871 26.5871 + C 0.32518 -0.85360 -4.42675 + C -1.07260 -0.83971 -4.34906 + C -1.73634 0.31773 -3.95111 + C -1.00588 1.46775 -3.62865 + C 0.38424 1.45396 -3.70593 + C 1.05168 0.29016 -4.10604 + H 0.84000 -1.75143 -4.73546 + H -1.63610 -1.72685 -4.59781 + H -1.52072 2.36559 -3.31996 + H 2.12992 0.27948 -4.16599 + O 1.09382 2.57111 -3.39269 + H 0.48991 3.27352 -3.14060 + C -3.24394 0.33266 -3.86731 + H -3.60252 1.32064 -4.06787 + H -3.64798 -0.34668 -4.58857 + H -3.54960 0.03464 -2.88615 +16 + Configuration number : 50000L = 26.5871 26.5871 26.5871 + C 0.32518 -0.85355 -4.42675 + C -1.07259 -0.83971 -4.34907 + C -1.73632 0.31774 -3.95113 + C -1.00589 1.46774 -3.62865 + C 0.38423 1.45395 -3.70591 + C 1.05165 0.29016 -4.10605 + H 0.83998 -1.75139 -4.73542 + H -1.63606 -1.72684 -4.59781 + H -1.52069 2.36555 -3.31997 + H 2.12987 0.27949 -4.16594 + O 1.09378 2.57107 -3.39267 + H 0.48989 3.27350 -3.14065 + C -3.24390 0.33267 -3.86733 + H -3.60249 1.32065 -4.06781 + H -3.64796 -0.34662 -4.58853 + H -3.54952 0.03464 -2.88618 +16 + Configuration number : 50000L = 26.5871 26.5871 26.5871 + C 0.32517 -0.85359 -4.42676 + C -1.07257 -0.83972 -4.34905 + C -1.73632 0.31775 -3.95112 + C -1.00588 1.46775 -3.62865 + C 0.38422 1.45395 -3.70592 + C 1.05166 0.29016 -4.10604 + H 0.84000 -1.75139 -4.73543 + H -1.63603 -1.72685 -4.59783 + H -1.52069 2.36555 -3.31999 + H 2.12991 0.27949 -4.16598 + O 1.09380 2.57108 -3.39267 + H 0.48990 3.27349 -3.14064 + C -3.24393 0.33268 -3.86732 + H -3.60255 1.32067 -4.06782 + H -3.64797 -0.34663 -4.58855 + H -3.54956 0.03464 -2.88617 +16 + Configuration number : 50000L = 26.5871 26.5871 26.5871 + C 0.32520 -0.85357 -4.42675 + C -1.07260 -0.83969 -4.34906 + C -1.73632 0.31774 -3.95111 + C -1.00591 1.46774 -3.62866 + C 0.38426 1.45396 -3.70591 + C 1.05165 0.29017 -4.10605 + H 0.84000 -1.75144 -4.73544 + H -1.63608 -1.72689 -4.59780 + H -1.52070 2.36553 -3.31997 + H 2.12996 0.27948 -4.16600 + O 1.09380 2.57106 -3.39269 + H 0.48989 3.27347 -3.14061 + C -3.24393 0.33268 -3.86732 + H -3.60246 1.32067 -4.06787 + H -3.64796 -0.34665 -4.58852 + H -3.54955 0.03462 -2.88619 +16 + Configuration number : 50000L = 26.5871 26.5871 26.5871 + C 0.32520 -0.85357 -4.42676 + C -1.07259 -0.83972 -4.34907 + C -1.73632 0.31775 -3.95110 + C -1.00590 1.46774 -3.62865 + C 0.38424 1.45396 -3.70591 + C 1.05168 0.29015 -4.10603 + H 0.84001 -1.75140 -4.73544 + H -1.63604 -1.72685 -4.59783 + H -1.52071 2.36556 -3.31998 + H 2.12996 0.27950 -4.16599 + O 1.09378 2.57108 -3.39271 + H 0.48987 3.27350 -3.14065 + C -3.24393 0.33269 -3.86730 + H -3.60249 1.32067 -4.06783 + H -3.64800 -0.34660 -4.58853 + H -3.54955 0.03464 -2.88622 +16 + Configuration number : 50000L = 26.5871 26.5871 26.5871 + C 0.32519 -0.85359 -4.42675 + C -1.07259 -0.83972 -4.34907 + C -1.73632 0.31775 -3.95111 + C -1.00589 1.46775 -3.62864 + C 0.38423 1.45396 -3.70592 + C 1.05167 0.29015 -4.10605 + H 0.84001 -1.75140 -4.73543 + H -1.63610 -1.72684 -4.59780 + H -1.52071 2.36557 -3.31997 + H 2.12998 0.27951 -4.16598 + O 1.09381 2.57110 -3.39268 + H 0.48988 3.27346 -3.14063 + C -3.24396 0.33266 -3.86732 + H -3.60252 1.32068 -4.06784 + H -3.64798 -0.34664 -4.58853 + H -3.54963 0.03460 -2.88617 +16 + Configuration number : 50000L = 26.5871 26.5871 26.5871 + C 0.32519 -0.85356 -4.42673 + C -1.07259 -0.83974 -4.34905 + C -1.73634 0.31773 -3.95111 + C -1.00590 1.46774 -3.62865 + C 0.38424 1.45396 -3.70593 + C 1.05166 0.29015 -4.10604 + H 0.83999 -1.75138 -4.73543 + H -1.63606 -1.72685 -4.59782 + H -1.52070 2.36554 -3.31998 + H 2.12997 0.27948 -4.16599 + O 1.09381 2.57109 -3.39269 + H 0.48988 3.27345 -3.14062 + C -3.24392 0.33269 -3.86732 + H -3.60253 1.32068 -4.06784 + H -3.64798 -0.34663 -4.58854 + H -3.54956 0.03460 -2.88618 +16 + Configuration number : 50000L = 26.5871 26.5871 26.5871 + C 0.32519 -0.85357 -4.42676 + C -1.07258 -0.83970 -4.34905 + C -1.73629 0.31777 -3.95113 + C -1.00588 1.46774 -3.62865 + C 0.38421 1.45394 -3.70593 + C 1.05165 0.29018 -4.10605 + H 0.83999 -1.75137 -4.73542 + H -1.63608 -1.72684 -4.59781 + H -1.52070 2.36556 -3.31997 + H 2.12993 0.27950 -4.16597 + O 1.09377 2.57105 -3.39267 + H 0.48988 3.27341 -3.14065 + C -3.24392 0.33269 -3.86729 + H -3.60250 1.32065 -4.06786 + H -3.64791 -0.34664 -4.58852 + H -3.54954 0.03464 -2.88618 +16 + Configuration number : 50000L = 26.5871 26.5871 26.5871 + C 0.32518 -0.85356 -4.42674 + C -1.07259 -0.83972 -4.34905 + C -1.73634 0.31774 -3.95111 + C -1.00590 1.46774 -3.62865 + C 0.38424 1.45395 -3.70593 + C 1.05168 0.29017 -4.10605 + H 0.83998 -1.75137 -4.73544 + H -1.63605 -1.72686 -4.59782 + H -1.52069 2.36555 -3.31998 + H 2.12994 0.27950 -4.16593 + O 1.09379 2.57107 -3.39269 + H 0.48990 3.27350 -3.14062 + C -3.24393 0.33268 -3.86732 + H -3.60246 1.32063 -4.06783 + H -3.64794 -0.34661 -4.58853 + H -3.54960 0.03463 -2.88615 +16 + Configuration number : 50000L = 26.5871 26.5871 26.5871 + C 0.32519 -0.85357 -4.42675 + C -1.07259 -0.83973 -4.34907 + C -1.73632 0.31775 -3.95110 + C -1.00590 1.46774 -3.62864 + C 0.38422 1.45396 -3.70593 + C 1.05168 0.29015 -4.10606 + H 0.83994 -1.75142 -4.73543 + H -1.63607 -1.72684 -4.59781 + H -1.52072 2.36555 -3.31998 + H 2.12995 0.27949 -4.16598 + O 1.09379 2.57109 -3.39267 + H 0.48989 3.27350 -3.14063 + C -3.24391 0.33268 -3.86731 + H -3.60250 1.32067 -4.06784 + H -3.64794 -0.34665 -4.58853 + H -3.54956 0.03461 -2.88620 diff --git a/othercontrol.in b/othercontrol.in new file mode 100644 index 0000000..0306cb4 --- /dev/null +++ b/othercontrol.in @@ -0,0 +1,11 @@ +initcyc = -4 pode? +maxcyc = 1 +forces = yes +nprocs = 2 + +# dice +#nmol = aslkj 1 20 slkdfj +dens = 0.75 +nsteps = 7000 2500 3876 +isave = 1340 +ljname = phb.pot diff --git a/phb.pot b/phb.pot new file mode 100644 index 0000000..976c15f --- /dev/null +++ b/phb.pot @@ -0,0 +1,51 @@ +* +2 +31 PHENOL BLUE geom/chg MP2/aug-cc-pVTZ Charge MK LJ OPLSAA + 1 6 -4.400337 0.665513 0.414312 -0.38759300 0.0700 3.5500 + 1 6 -4.499567 -0.672788 -0.153273 0.80400100 0.0700 3.5500 + 1 6 -3.256300 -1.289216 -0.613514 -0.33849100 0.0700 3.5500 + 1 6 -2.058491 -0.668069 -0.486739 -0.22078300 0.0700 3.5500 + 1 6 -1.971143 0.651479 0.105111 0.56352700 0.0700 3.5500 + 1 6 -3.206008 1.296843 0.497122 -0.14537200 0.0700 3.5500 + 2 8 -5.594533 -1.253085 -0.287655 -0.71446100 0.2100 2.9600 + 3 7 -0.874044 1.358704 0.276359 -0.72179200 0.1700 3.2500 + 4 6 0.387854 0.815120 0.144104 0.60712300 0.0700 3.5500 + 4 6 1.407755 1.658002 -0.332615 -0.29547600 0.0700 3.5500 + 4 6 0.759497 -0.468150 0.587914 -0.34666100 0.0700 3.5500 + 4 6 2.710211 1.215186 -0.461194 -0.29854600 0.0700 3.5500 + 4 6 2.073539 -0.898835 0.508310 -0.23428400 0.0700 3.5500 + 4 6 3.080760 -0.089365 -0.061116 0.29465100 0.0700 3.5500 + 5 7 4.372382 -0.539792 -0.201825 -0.19049700 0.1700 3.2500 + 6 6 5.419802 0.438244 -0.438362 -0.21318300 0.0660 3.5000 + 6 6 4.763609 -1.735216 0.522254 -0.22542000 0.0660 3.5000 + 7 1 6.366998 -0.085365 -0.519616 0.10984000 0.0300 2.5000 + 7 1 5.251961 0.966123 -1.374211 0.07714000 0.0300 2.5000 + 7 1 5.495169 1.174115 0.367485 0.12575800 0.0300 2.5000 + 7 1 4.158375 -2.584419 0.214461 0.08322900 0.0300 2.5000 + 7 1 5.796953 -1.962538 0.280411 0.11536100 0.0300 2.5000 + 7 1 4.674161 -1.617074 1.606614 0.12144000 0.0300 2.5000 + 7 1 0.028134 -1.095538 1.080074 0.17943400 0.0300 2.4200 + 7 1 2.318762 -1.865762 0.919126 0.17725000 0.0300 2.4200 + 7 1 3.451018 1.898797 -0.846692 0.19884400 0.0300 2.4200 + 7 1 1.147588 2.669090 -0.614979 0.17338800 0.0300 2.4200 + 7 1 -3.119300 2.296790 0.900595 0.15153400 0.0300 2.4200 + 7 1 -5.315819 1.136106 0.744794 0.20528900 0.0300 2.4200 + 7 1 -3.338131 -2.250367 -1.102310 0.18436700 0.0300 2.4200 + 7 1 -1.163740 -1.117915 -0.893805 0.16038200 0.0300 2.4200 +16 + 1 6 0.672026 -2.823446 0.002631 -0.11500000 0.0700 3.5500 + 1 6 2.072026 -2.823446 0.002631 -0.11500000 0.0700 3.5500 + 1 6 2.768235 -1.617645 0.002633 -0.11500000 0.0700 3.5500 + 1 6 2.068235 -0.405210 0.002635 -0.11500000 0.0700 3.5500 + 1 14 0.675894 -0.405219 0.002635 0.15000000 0.0700 3.5500 + 1 104 -0.024198 -1.617602 0.002633 -0.11500000 0.0700 3.5500 + 2 1 0.132026 -3.758753 0.002629 0.11500000 0.0300 2.4200 + 2 1 2.612026 -3.758753 0.002629 0.11500000 0.0300 2.4200 + 2 1 2.608235 0.530098 0.002636 0.11500000 0.0300 2.4200 + 2 1 -1.104198 -1.617602 0.002633 0.11500000 0.0300 2.4200 + 3 8 -0.004114 0.772571 0.002637 -0.58500000 0.1700 3.0700 + 3 1 0.619778 1.502200 0.002638 0.43500000 0.0000 0.0000 + 4 6 4.278235 -1.617645 0.002633 0.11500000 0.1700 3.8000 + 4 1 4.634902 -0.743994 0.507036 0.00000000 0.0000 0.0000 + 4 1 4.634902 -2.491297 0.507036 0.00000000 0.0000 0.0000 + 4 1 4.634902 -1.617645 -1.006173 0.00000000 0.0000 0.0000 diff --git a/phb.xyz.last-p01 b/phb.xyz.last-p01 new file mode 100644 index 0000000..baa2f94 --- /dev/null +++ b/phb.xyz.last-p01 @@ -0,0 +1,1633 @@ + 1631 + Configuration number : 50000L = 26.5871 26.5871 26.5871 + C -4.39451 0.69877 0.42135 + C -4.50462 -0.64085 -0.14109 + C -3.26684 -1.26791 -0.60175 + C -2.06431 -0.65497 -0.47984 + C -1.96616 0.66607 0.10697 + C -3.19548 1.32176 0.49927 + O -5.60404 -1.21371 -0.27098 + N -0.86362 1.36598 0.27325 + C 0.39404 0.81282 0.14027 + C 1.41894 1.64657 -0.34174 + C 0.75738 -0.47146 0.58799 + C 2.71789 1.19390 -0.47150 + C 2.06811 -0.91191 0.50714 + C 3.07989 -0.11182 -0.06743 + N 4.36793 -0.57207 -0.20927 + C 5.42185 0.39750 -0.45166 + C 4.75210 -1.76763 0.51835 + H 6.36507 -0.13322 -0.53303 + H 5.25578 0.92315 -1.38908 + H 5.50428 1.13576 0.35131 + H 4.14009 -2.61357 0.21499 + H 5.78325 -2.00329 0.27512 + H 4.66588 -1.64488 1.60246 + H 0.02259 -1.09175 1.08403 + H 2.30725 -1.87907 0.92097 + H 3.46276 1.87073 -0.86111 + H 1.16546 2.65847 -0.62726 + H -3.10068 2.32253 0.89887 + H -5.30585 1.17717 0.75208 + H -3.35667 -2.23023 -1.08683 + H -1.17372 -1.11275 -0.88718 + C 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H -3.45045 12.24109 10.03430 + C -10.85392 -12.99372 -2.78794 + C -10.21338 -13.92914 -3.60934 + C -10.37640 -13.86971 -4.99084 + C -11.18089 -12.87448 -5.55855 + Si -11.81795 -11.94416 -4.74166 + XX -11.65404 -12.00386 -3.35257 + H -10.72746 -13.03985 -1.71642 + H -9.59276 -14.69688 -3.17142 + H -11.30739 -12.82835 -6.63013 + H -12.14818 -11.28225 -2.71894 + O -12.59944 -10.97737 -5.29312 + H -12.60541 -11.07675 -6.24795 + C -9.68553 -14.87866 -5.87676 + H -9.47056 -14.43245 -6.82525 + H -8.77269 -15.19267 -5.41519 + H -10.32379 -15.72578 -6.01763 + C 9.82181 5.34170 11.35239 + C 10.52097 4.25193 11.88494 + C 11.69031 4.46247 12.61086 + C 12.16692 5.76399 12.80819 + Si 11.47159 6.84778 12.27853 + XX 10.29582 6.63615 11.54860 + H 8.91479 5.17835 10.78930 + H 10.15329 3.24790 11.73274 + H 13.07395 5.92732 13.37123 + H 9.75646 7.47685 11.13777 + O 11.93458 8.11207 12.47022 + H 12.74333 8.08180 12.98655 + C 12.44439 3.28712 13.18526 + H 12.94798 3.58908 14.07972 + H 11.75729 2.49870 13.41164 + H 13.16227 2.94061 12.47144 + C -13.54648 12.36520 6.34988 + C -14.11940 11.09750 6.50676 + C -13.32004 10.00951 6.84725 + C -11.94331 10.18327 7.03270 + Si -11.37350 11.44405 6.87669 + XX -12.17720 12.53806 6.53433 + H -14.16650 13.20914 6.08580 + H -15.18144 10.96344 6.36369 + H -11.32324 9.33940 7.29680 + H -11.73519 13.51601 6.41332 + O -10.03611 11.61288 7.05685 + H -9.63533 10.77106 7.28555 + C -13.93803 8.64217 7.01646 + H -13.37629 8.08343 7.73563 + H -14.94752 8.74647 7.35533 + H -13.92803 8.12770 6.07833 + C 10.39058 9.66478 -9.88481 + C 9.35618 8.80753 -10.27867 + C 9.00218 8.71496 -11.62207 + C 9.68068 9.47907 -12.57902 + Si 10.70943 10.33161 -12.18729 + XX 11.06542 10.42478 -10.83652 + H 10.66515 9.73658 -8.84282 + H 8.83277 8.21805 -9.54047 + H 9.40611 9.40726 -13.62107 + H 11.86339 11.08608 -10.53267 + O 11.36852 11.07393 -13.11687 + H 11.00462 10.89384 -13.98674 + C 7.88652 7.79036 -12.04690 + H 8.07239 7.44019 -13.04074 + H 7.83997 6.95668 -11.37785 + H 6.95656 8.31913 -12.02314 + C 7.50876 13.75031 10.12910 + C 8.15515 14.20541 11.28456 + C 8.29501 13.36079 12.38259 + C 7.78920 12.05635 12.33119 + Si 7.14634 11.60376 11.18206 + XX 7.00571 12.45299 10.07796 + H 7.40032 14.40552 9.27746 + H 8.54534 15.21167 11.32422 + H 7.89766 11.40119 13.18289 + H 6.50705 12.10189 9.18663 + O 6.65496 10.33657 11.13210 + H 6.83317 9.89141 11.96374 + C 8.99218 13.85162 13.62882 + H 9.46622 13.02784 14.12032 + H 9.72939 14.57977 13.36178 + H 8.27504 14.29519 14.28749 + C 14.32030 11.77539 -8.95573 + C 14.67114 10.79423 -8.02073 + C 13.83805 10.53760 -6.93503 + C 12.64954 11.26070 -6.77840 + Si 12.30063 12.23650 -7.70831 + XX 13.13825 12.49461 -8.79998 + H 14.96651 11.97444 -9.79785 + H 15.58800 10.23642 -8.14155 + H 12.00332 11.06165 -5.93628 + H 12.86760 13.25152 -9.52129 + O 11.14610 12.93893 -7.55617 + H 10.69277 12.64165 -6.76390 + C 14.21644 9.47935 -5.92655 + H 13.32922 9.05035 -5.50973 + H 14.78925 8.71525 -6.40920 + H 14.79897 9.92253 -5.14608 + C -9.95511 9.03486 -12.01981 + C -9.90897 10.40466 -12.30530 + C -11.09018 11.13463 -12.40769 + C -12.32404 10.49881 -12.22517 + Si -12.36992 9.13650 -11.94125 + XX -11.18226 8.40245 -11.83825 + H -9.03888 8.46863 -11.94039 + H -8.95714 10.89516 -12.44611 + H -13.24028 11.06502 -12.30459 + H -11.21784 7.34577 -11.61801 + O -13.56851 8.51885 -11.76392 + H -14.27662 9.15879 -11.86720 + C -11.04041 12.61207 -12.71563 + H -11.88078 13.09855 -12.26616 + H -10.13585 13.02783 -12.32351 + H -11.06940 12.75668 -13.77539 + C 12.25406 13.28263 9.47645 + C 11.16910 12.40549 9.59278 + C 11.36191 11.12289 10.09916 + C 12.64078 10.71040 10.49204 + Si 13.71979 11.58273 10.37639 + XX 13.52597 12.87239 9.86721 + H 12.10448 14.27747 9.08365 + H 10.18257 12.72369 9.28967 + H 12.79037 9.71555 10.88484 + H 14.36294 13.54900 9.77750 + O 14.96209 11.18203 10.75805 + H 14.92179 10.27900 11.08131 + C 10.19177 10.17687 10.22459 + H 10.35778 9.51103 11.04553 + H 9.29652 10.73754 10.39553 + H 10.09166 9.61170 9.32155 + C -13.46371 -9.55060 -14.69307 + C -13.56015 -10.66741 -13.85435 + C -13.42708 -10.51694 -12.47657 + C -13.19679 -9.24879 -11.92994 + Si -13.10085 -8.13813 -12.76409 + XX -13.23468 -8.28936 -14.14945 + H -13.56697 -9.66737 -15.76178 + H -13.73780 -11.64570 -14.27599 + H -13.09355 -9.13205 -10.86124 + H -13.16029 -7.42782 -14.79647 + O -12.87718 -6.90621 -12.23308 + H -12.81061 -6.97678 -11.27801 + C -13.53113 -11.72146 -11.57192 + H -13.92198 -11.42150 -10.62210 + H -14.18433 -12.44435 -12.01424 + H -12.56074 -12.15211 -11.43838 diff --git a/run.log b/run.log new file mode 100644 index 0000000..0be58a8 --- /dev/null +++ b/run.log @@ -0,0 +1,229 @@ +########################################################################################## +############# Welcome to DICEPLAYER version 1.0 ############# +########################################################################################## + +Your python version is 3.6.1 (default, Apr 24 2017, 06:18:27) +[GCC 4.2.1 Compatible Apple LLVM 8.0.0 (clang-800.0.42.1)] + +Program started on Wednesday, 14 Jun 2017 at 12:30:02 + +Environment variables: +OMP_STACKSIZE = 32M + +========================================================================================== + CONTROL variables being used in this run: +------------------------------------------------------------------------------------------ + +altsteps = 20000 +ghosts = no +initcyc = 1 +lps = no +maxcyc = 3 +maxstep = 0.3 +nprocs = 2 +opt = no +qmprog = g09 +switch_step = 3 +zipprog = gzip + +------------------------------------------------------------------------------------------ + DICE variables being used in this run: +------------------------------------------------------------------------------------------ + +dens = 0.75 +isave = 1000 +ljname = phb.pot +ncores = 1 +nmol = 1 100 +nstep = 40000 60000 50000 +outname = phb +press = 1.0 +temp = 300.0 +title = Diceplayer run + +------------------------------------------------------------------------------------------ + GAUSSIAN variables being used in this run: +------------------------------------------------------------------------------------------ + +chgmult = 0 1 +level = MP2/aug-cc-pVTZ +pop = chelpg + + +========================================================================================== + +Program dice found at /usr/local/bin/dice + +========================================================================================== + Potential parameters from file phb.pot: +------------------------------------------------------------------------------------------ + +Combination rule: * +Types of molecules: 2 + +31 atoms in molecule type 1: +--------------------------------------------------------------------------------- +Lbl AN X Y Z Charge Epsilon Sigma Mass +--------------------------------------------------------------------------------- +1 6 -4.40034 0.66551 0.41431 -0.387593 0.07000 3.5500 12.0110 +1 6 -4.49957 -0.67279 -0.15327 0.804001 0.07000 3.5500 12.0110 +1 6 -3.25630 -1.28922 -0.61351 -0.338491 0.07000 3.5500 12.0110 +1 6 -2.05849 -0.66807 -0.48674 -0.220783 0.07000 3.5500 12.0110 +1 6 -1.97114 0.65148 0.10511 0.563527 0.07000 3.5500 12.0110 +1 6 -3.20601 1.29684 0.49712 -0.145372 0.07000 3.5500 12.0110 +2 8 -5.59453 -1.25309 -0.28765 -0.714461 0.21000 2.9600 15.9990 +3 7 -0.87404 1.35870 0.27636 -0.721792 0.17000 3.2500 14.0070 +4 6 0.38785 0.81512 0.14410 0.607123 0.07000 3.5500 12.0110 +4 6 1.40776 1.65800 -0.33261 -0.295476 0.07000 3.5500 12.0110 +4 6 0.75950 -0.46815 0.58791 -0.346661 0.07000 3.5500 12.0110 +4 6 2.71021 1.21519 -0.46119 -0.298546 0.07000 3.5500 12.0110 +4 6 2.07354 -0.89884 0.50831 -0.234284 0.07000 3.5500 12.0110 +4 6 3.08076 -0.08936 -0.06112 0.294651 0.07000 3.5500 12.0110 +5 7 4.37238 -0.53979 -0.20183 -0.190497 0.17000 3.2500 14.0070 +6 6 5.41980 0.43824 -0.43836 -0.213183 0.06600 3.5000 12.0110 +6 6 4.76361 -1.73522 0.52225 -0.225420 0.06600 3.5000 12.0110 +7 1 6.36700 -0.08536 -0.51962 0.109840 0.03000 2.5000 1.0079 +7 1 5.25196 0.96612 -1.37421 0.077140 0.03000 2.5000 1.0079 +7 1 5.49517 1.17412 0.36749 0.125758 0.03000 2.5000 1.0079 +7 1 4.15838 -2.58442 0.21446 0.083229 0.03000 2.5000 1.0079 +7 1 5.79695 -1.96254 0.28041 0.115361 0.03000 2.5000 1.0079 +7 1 4.67416 -1.61707 1.60661 0.121440 0.03000 2.5000 1.0079 +7 1 0.02813 -1.09554 1.08007 0.179434 0.03000 2.4200 1.0079 +7 1 2.31876 -1.86576 0.91913 0.177250 0.03000 2.4200 1.0079 +7 1 3.45102 1.89880 -0.84669 0.198844 0.03000 2.4200 1.0079 +7 1 1.14759 2.66909 -0.61498 0.173388 0.03000 2.4200 1.0079 +7 1 -3.11930 2.29679 0.90060 0.151534 0.03000 2.4200 1.0079 +7 1 -5.31582 1.13611 0.74479 0.205289 0.03000 2.4200 1.0079 +7 1 -3.33813 -2.25037 -1.10231 0.184367 0.03000 2.4200 1.0079 +7 1 -1.16374 -1.11791 -0.89380 0.160382 0.03000 2.4200 1.0079 + +16 atoms in molecule type 2: +--------------------------------------------------------------------------------- +Lbl AN X Y Z Charge Epsilon Sigma Mass +--------------------------------------------------------------------------------- +1 6 0.67203 -2.82345 0.00263 -0.115000 0.07000 3.5500 12.0110 +1 6 2.07203 -2.82345 0.00263 -0.115000 0.07000 3.5500 12.0110 +1 6 2.76823 -1.61764 0.00263 -0.115000 0.07000 3.5500 12.0110 +1 6 2.06824 -0.40521 0.00264 -0.115000 0.07000 3.5500 12.0110 +1 14 0.67589 -0.40522 0.00264 0.150000 0.07000 3.5500 28.0860 +1 104 -0.02420 -1.61760 0.00263 -0.115000 0.07000 3.5500 0.0000 +2 1 0.13203 -3.75875 0.00263 0.115000 0.03000 2.4200 1.0079 +2 1 2.61203 -3.75875 0.00263 0.115000 0.03000 2.4200 1.0079 +2 1 2.60824 0.53010 0.00264 0.115000 0.03000 2.4200 1.0079 +2 1 -1.10420 -1.61760 0.00263 0.115000 0.03000 2.4200 1.0079 +3 8 -0.00411 0.77257 0.00264 -0.585000 0.17000 3.0700 15.9990 +3 1 0.61978 1.50220 0.00264 0.435000 0.00000 0.0000 1.0079 +4 6 4.27823 -1.61764 0.00263 0.115000 0.17000 3.8000 12.0110 +4 1 4.63490 -0.74399 0.50704 0.000000 0.00000 0.0000 1.0079 +4 1 4.63490 -2.49130 0.50704 0.000000 0.00000 0.0000 1.0079 +4 1 4.63490 -1.61764 -1.00617 0.000000 0.00000 0.0000 1.0079 + + +========================================================================================== + +Molecule type 1: + + Center of mass = ( -0.0000 , 0.0000 , 0.0000 ) + Moments of inertia = 3.144054E+02 2.801666E+03 3.027366E+03 + Major principal axis = ( 0.999972 , 0.007210 , 0.002184 ) + Inter principal axis = ( -0.007218 , 0.999967 , 0.003660 ) + Minor principal axis = ( -0.002157 , -0.003676 , 0.999991 ) + Characteristic lengths = ( 11.96 , 5.25 , 2.98 ) + Total mass = 226.28 au + Total charge = -0.0000 e + Dipole moment = ( 9.8367 , 0.6848 , 0.8358 ) Total = 9.8959 Debye + + Translating and rotating molecule to standard orientation... Done + + New values: + Center of mass = ( -0.0000 , 0.0000 , -0.0000 ) + Moments of inertia = 3.144054E+02 2.801666E+03 3.027366E+03 + Major principal axis = ( 1.000000 , 0.000000 , 0.000000 ) + Inter principal axis = ( -0.000000 , 1.000000 , -0.000000 ) + Minor principal axis = ( 0.000000 , 0.000000 , 1.000000 ) + Characteristic lengths = ( 11.97 , 5.27 , 2.99 ) + Total mass = 226.28 au + Total charge = -0.0000 e + Dipole moment = ( 9.8432 , 0.6168 , 0.8120 ) Total = 9.8959 Debye + + +Molecule type 2: + + Center of mass = ( 1.6067 , -1.0929 , 0.0026 ) + Moments of inertia = 1.205279E+02 2.859254E+02 4.033761E+02 + Major principal axis = ( 0.795913 , -0.605411 , -0.000001 ) + Inter principal axis = ( 0.605411 , 0.795913 , 0.000001 ) + Minor principal axis = ( 0.000000 , -0.000002 , 1.000000 ) + Characteristic lengths = ( 5.74 , 5.26 , 1.51 ) + Total mass = 112.20 au + Total charge = -0.0000 e + Dipole moment = ( 2.3293 , 0.1593 , -0.0000 ) Total = 2.3347 Debye + + Translating and rotating molecule to standard orientation... Done + + New values: + Center of mass = ( 0.0000 , 0.0000 , 0.0000 ) + Moments of inertia = 1.205279E+02 2.859254E+02 4.033761E+02 + Major principal axis = ( -1.000000 , 0.000000 , 0.000000 ) + Inter principal axis = ( 0.000000 , 1.000000 , 0.000000 ) + Minor principal axis = ( 0.000000 , 0.000000 , 1.000000 ) + Characteristic lengths = ( 5.67 , 5.13 , 1.51 ) + Total mass = 112.20 au + Total charge = -0.0000 e + Dipole moment = ( 1.7575 , 1.5369 , -0.0000 ) Total = 2.3347 Debye + +========================================================================================== + +Starting the iterative process. + +------------------------------------------------------------------------------------------ + Step # 1 +------------------------------------------------------------------------------------------ + +Simulation process p01 initiated with pid 6822 +Simulation process p02 initiated with pid 6823 +p01> NVT thermalization initiated (from random configuration) on 14 Jun 2017 at 12:30:02 +p02> NVT thermalization initiated (from random configuration) on 14 Jun 2017 at 12:30:02 +p02> NPT thermalization initiated on 14 Jun 2017 at 12:41:16 +p01> NPT thermalization initiated on 14 Jun 2017 at 12:41:17 +p02> NPT production initiated on 14 Jun 2017 at 13:01:25 +p01> NPT production initiated on 14 Jun 2017 at 13:01:27 +p02> ----- NPT production finished on 14 Jun 2017 at 13:57:41 +p01> ----- NPT production finished on 14 Jun 2017 at 13:57:53 + +Building the ASEC and vdW meanfields... In average, 99.97 molecules were selected from the production simulations to form the +ASEC comprising a shell with minimum thickness of 15.352263400006278 AngstromDone. + +------------------------------------------------------------------------------------------ + Step # 2 +------------------------------------------------------------------------------------------ + +Simulation process p01 initiated with pid 6903 +Simulation process p02 initiated with pid 6904 +p02> NPT thermalization initiated (from previous configuration) on 14 Jun 2017 at 13:58:52 +p01> NPT thermalization initiated (from previous configuration) on 14 Jun 2017 at 13:58:52 +p02> NPT production initiated on 14 Jun 2017 at 14:05:14 +p01> NPT production initiated on 14 Jun 2017 at 14:05:20 +p02> ----- NPT production finished on 14 Jun 2017 at 14:23:58 +p01> ----- NPT production finished on 14 Jun 2017 at 14:24:05 + +Building the ASEC and vdW meanfields... In average, 99.66 molecules were selected from the production simulations to form the +ASEC comprising a shell with minimum thickness of 14.942583400006276 AngstromDone. + +------------------------------------------------------------------------------------------ + Step # 3 +------------------------------------------------------------------------------------------ + +Simulation process p01 initiated with pid 6945 +p01> NPT thermalization initiated (from previous configuration) on 14 Jun 2017 at 14:24:45 +Simulation process p02 initiated with pid 6946 +p02> NPT thermalization initiated (from previous configuration) on 14 Jun 2017 at 14:24:45 +p02> NPT production initiated on 14 Jun 2017 at 14:31:05 +p01> NPT production initiated on 14 Jun 2017 at 14:31:06 +p02> ----- NPT production finished on 14 Jun 2017 at 14:48:15 +p01> ----- NPT production finished on 14 Jun 2017 at 14:48:15 + +Building the ASEC and vdW meanfields... In average, 99.0 molecules were selected from the production simulations to form the +ASEC comprising a shell with minimum thickness of 14.79446440000628 AngstromDone. + +Diceplayer finished normally! \ No newline at end of file diff --git a/test4.py b/test4.py new file mode 100644 index 0000000..ec31de5 --- /dev/null +++ b/test4.py @@ -0,0 +1,64 @@ +#!/opt/local/bin/python3 + +import sys, math +from math import pi +import numpy as np +from numpy import linalg +from numpy.random import rand, random +from copy import deepcopy + +from DPpack.MolHandling import * +from DPpack.PTable import * + + +natoms = input("# of atoms: ") +natoms = int(natoms) +file = input("xyz file: ") + +molecules=[] + +with open(file) as fh: + xyzfile = fh.readlines() + +file += ".new" +file2 = file + "2" +fh = open(file, "w") +fh2 = open(file2, "w") + +total_atoms = int(xyzfile.pop(0).split()[0]) +fh.write("{}\n".format(total_atoms)) +comment = xyzfile.pop(0) +fh.write("{}".format(comment)) + +nmols = round(total_atoms/natoms) +for i in range(nmols): + molecules.append([]) + for j in range(natoms): + molecules[i].append({}) + line = xyzfile.pop(0).split() + molecules[i][j]['na'] = int(line[0]) + molecules[i][j]['rx'] = float(line[1]) + molecules[i][j]['ry'] = float(line[2]) + molecules[i][j]['rz'] = float(line[3]) + molecules[i][j]['mass'] = atommass[molecules[0][j]['na']] + +for atom in molecules[0]: + fh.write("{:>4s} {:>11.5f} {:>11.5f} {:>11.5f}\n".format(atomsymb[atom['na']], + atom['rx'], atom['ry'], atom['rz'])) + fh2.write("{:>4s} {:>11.5f} {:>11.5f} {:>11.5f}\n".format(atomsymb[atom['na']], + atom['rx'], atom['ry'], atom['rz'])) + +for i in range(1, nmols): + fh2.write("{}\n".format(natoms)) + fh2.write("{}".format(comment)) + rmsd, projected_mol = rmsd_fit(molecules[i], molecules[0]) + print("{:>9.5f}".format(rmsd)) + for atom in projected_mol: + fh.write("{:>4s} {:>11.5f} {:>11.5f} {:>11.5f}\n".format(atomsymb[atom['na']], + atom['rx'], atom['ry'], atom['rz'])) + fh2.write("{:>4s} {:>11.5f} {:>11.5f} {:>11.5f}\n".format(atomsymb[atom['na']], + atom['rx'], atom['ry'], atom['rz'])) + +fh.close() +fh2.close() +