348
DPpack/Molcas.py
Normal file
348
DPpack/Molcas.py
Normal file
@@ -0,0 +1,348 @@
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import os, sys
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import textwrap
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import subprocess
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from DPpack.PTable import *
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from DPpack.SetGlobals import *
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from DPpack.MolHandling import *
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from DPpack.Misc import *
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|
||||
####################################### functions ######################################
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def read_forces_log(file, fh):
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||||
|
||||
forces = []
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try:
|
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with open(file) as tmpfh:
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logfile = tmpfh.readlines()
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except:
|
||||
sys.exit("Error: cannot open file {}".format(file))
|
||||
|
||||
start = logfile.pop(0).strip()
|
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while start.find("Molecular gradients") < 0: ## expression not found
|
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start = logfile.pop(0).strip()
|
||||
|
||||
logfile = logfile[7:] ## skip next 7 lines
|
||||
|
||||
for i in range(len(molecules[0])):
|
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values = logfile.pop(0).split()
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values = values[1:]
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forces.extend([ float(x) for x in values ])
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gradient = np.array(forces)
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fh.write("\nGradient read from file {}:\n".format(file))
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fh.write("-----------------------------------------------------------------------\n"
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"Center Atomic Forces (Hartree/Bohr)\n"
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"Number Number X Y Z\n"
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"-----------------------------------------------------------------------\n")
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for i in range(len(molecules[0])):
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fh.write(" {:>5d} {:>3d} {:>14.9f} {:>14.9f} {:>14.9f}\n".format(
|
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i + 1, molecules[0][i]['na'], forces.pop(0), forces.pop(0), forces.pop(0)))
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||||
|
||||
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))
|
||||
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||||
start = logfile.pop(0).strip()
|
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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:
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||||
for charge in asec_charges:
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||||
fh.write("{:>10.5f} {:>10.5f} {:>10.5f} {:>11.8f} 0.0 0.0 0.0\n".format(
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||||
charge['rx'], charge['ry'], charge['rz'], charge['chg']))
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||||
|
||||
fh.write("End of input\n")
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||||
fh.close()
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||||
|
||||
return
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||||
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||||
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def make_force_input(cycle, asec_charges):
|
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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")
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||||
fh.write(" Coord\n")
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||||
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nsites = len(molecules[0])
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if cycle >= player['switchcyc']:
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nsites += len(ghost_atoms) + len(lp_atoms)
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fh.write("{}\n".format(nsites))
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||||
fh.write("\nForce calculation - Cycle number {}\n".format(cycle))
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||||
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||||
for atom in molecules[0]:
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||||
symbol = atomsymb[atom['na']]
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fh.write("{:<2s} {:>10.5f} {:>10.5f} {:>10.5f}\n".format(symbol,
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atom['rx'], atom['ry'], atom['rz']))
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## If also performing charge fit in the same calculation
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if cycle >= player['switchcyc']:
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for ghost in ghost_atoms:
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fh.write("Bq {:>10.5f} {:>10.5f} {:>10.5f}\n".format(
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ghost['rx'], ghost['ry'], ghost['rz']))
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for lp in lp_atoms:
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||||
fh.write("Bq {:>10.5f} {:>10.5f} {:>10.5f}\n".format(
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lp['rx'], lp['ry'], lp['rz']))
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||||
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||||
fh.write("basis = {}\n".format(molcas['basis']))
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||||
fh.write("group= nosym\n")
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||||
fh.write(" XFIELD\n")
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fh.write(">>> Include asec.xfield\n")
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||||
if not os.path.isfile(molcas['mbottom']):
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sys.exit("Error: cannot find file {} in main directory".format(molcas['mbottom']))
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||||
try:
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||||
with open(molcas['mbottom']) as mbottomfile:
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||||
mbottom = mbottomfile.readlines()
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||||
except:
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||||
sys.exit("Error: cannot open file {}".format(molcas['mbottom']))
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||||
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for line in mbottom:
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fh.write(line)
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fh.write(" &Alaska\nPNEW\n &SLAPAF\nCartesian\n")
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fh.close()
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return
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||||
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||||
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def make_charge_input(cycle, asec_charges):
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path = "step{:02d}".format(cycle) + os.sep + "qm"
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file = path + os.sep + "asec.input"
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||||
try:
|
||||
fh = open(file, "w")
|
||||
except:
|
||||
sys.exit("Error: cannot open file {}".format(file))
|
||||
|
||||
fh.write(" &Gateway\n")
|
||||
fh.write(" Coord\n")
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||||
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||||
nsites = len(molecules[0])
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if cycle >= player['switchcyc']:
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nsites += len(ghost_atoms) + len(lp_atoms)
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fh.write("{}\n".format(nsites))
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||||
fh.write("\nForce calculation - Cycle number {}\n".format(cycle))
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||||
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||||
for atom in molecules[0]:
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symbol = atomsymb[atom['na']]
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||||
fh.write("{:<2s} {:>10.5f} {:>10.5f} {:>10.5f}\n".format(symbol,
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||||
atom['rx'], atom['ry'], atom['rz']))
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||||
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for ghost in ghost_atoms:
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fh.write("Bq {:>10.5f} {:>10.5f} {:>10.5f}\n".format(
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ghost['rx'], ghost['ry'], ghost['rz']))
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||||
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||||
for lp in lp_atoms:
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fh.write("Bq {:>10.5f} {:>10.5f} {:>10.5f}\n".format(
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||||
lp['rx'], lp['ry'], lp['rz']))
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||||
|
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fh.write("basis = {}\n".format(molcas['basis']))
|
||||
fh.write("group= nosym\n")
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||||
fh.write(" XFIELD\n")
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||||
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
|
||||
|
||||
|
||||
|
||||
Reference in New Issue
Block a user