From 8cf9188c6d891561c99f85191f3e55fc3db56db9 Mon Sep 17 00:00:00 2001 From: Vitor Hideyoshi Date: Mon, 21 Feb 2022 13:31:17 +0000 Subject: [PATCH] Creation of Binary with cx_Freeze --- diceplayer/DPpack/SetGlobals.py | 2 +- diceplayer/__main__.py | 6 +- geoms.xyz | 15 +++ run.log | 184 ++++++++++++++++++++++++++++++++ run.log.backup | 169 +++++++++++++++++++++++++++++ setup.py | 17 +++ 6 files changed, 389 insertions(+), 4 deletions(-) create mode 100644 geoms.xyz create mode 100644 run.log create mode 100644 run.log.backup create mode 100644 setup.py diff --git a/diceplayer/DPpack/SetGlobals.py b/diceplayer/DPpack/SetGlobals.py index a51744e..1495eb9 100644 --- a/diceplayer/DPpack/SetGlobals.py +++ b/diceplayer/DPpack/SetGlobals.py @@ -2,7 +2,7 @@ from diceplayer.DPpack.MolHandling import * from diceplayer.DPpack.PTable import * from diceplayer.DPpack.Misc import * -from diceplayer.DPpack.runtime.Dice import * +from diceplayer.DPpack.external.Dice import * from typing import IO, Tuple, List, TextIO, Union diff --git a/diceplayer/__main__.py b/diceplayer/__main__.py index 1cdcc37..2fb788e 100644 --- a/diceplayer/__main__.py +++ b/diceplayer/__main__.py @@ -13,8 +13,8 @@ from diceplayer.DPpack.SetGlobals import * from diceplayer.DPpack.MolHandling import * from diceplayer.DPpack.Misc import * -_version = 'dev' -setproctitle.setproctitle("diceplayer-{}".format(_version)) +__version = 'dev' +setproctitle.setproctitle("diceplayer-{}".format(__version)) if __name__ == '__main__': #### Read and store the arguments passed to the program #### @@ -22,7 +22,7 @@ if __name__ == '__main__': parser = argparse.ArgumentParser(prog='Diceplayer') parser.add_argument('--continue', dest='opt_continue' , default=False, action='store_true') - parser.add_argument('--version', action='version', version='%(prog)s 1.0') + parser.add_argument('--version', action='version', version= "diceplayer-"+__version) 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', diff --git a/geoms.xyz b/geoms.xyz new file mode 100644 index 0000000..d2cf318 --- /dev/null +++ b/geoms.xyz @@ -0,0 +1,15 @@ +Cycle # 0 +Number of site: 12 +C 1.400000 0.000000 0.000000 +C 0.700000 1.212436 0.000000 +C -0.700000 1.212436 0.000000 +C -1.400000 0.000000 0.000000 +C -0.700000 -1.212436 0.000000 +C 0.700000 -1.212436 0.000000 +H 2.488100 0.000000 0.000000 +H 1.244000 2.154671 0.000000 +H -1.244000 2.154671 0.000000 +H -2.488100 0.000000 0.000000 +H -1.244000 -2.154671 0.000000 +H 1.244000 -2.154671 0.000000 +---------------------------------------- diff --git a/run.log b/run.log new file mode 100644 index 0000000..2493e7e --- /dev/null +++ b/run.log @@ -0,0 +1,184 @@ +########################################################################################## +############# Welcome to DICEPLAYER version 1.0 ############# +########################################################################################## + +Your python version is 3.8.12 | packaged by conda-forge | (default, Oct 12 2021, 21:57:06) +[GCC 9.4.0] + +Program started on Monday, 21 Feb 2022 at 13:19:54 + +Environment variables: +OMP_STACKSIZE = Not set + +========================================================================================== + CONTROL variables being used in this run: +------------------------------------------------------------------------------------------ + +altsteps = 20000 +freq = no +ghosts = no +initcyc = 1 +lps = no +maxcyc = 3 +maxstep = 0.3 +nprocs = 4 +opt = no +qmprog = g16 +readhessian = no +switchcyc = 3 +tol_factor = 1.2 +vdwforces = no + +------------------------------------------------------------------------------------------ + DICE variables being used in this run: +------------------------------------------------------------------------------------------ + +combrule = * +dens = 0.75 +infile = <_io.TextIOWrapper name='control.in' mode='r' encoding='UTF-8'> +isave = 1000 +ljname = phb.ljc +ncores = 3 +nmol = 1 50 +nstep = 20000 20000 +outfile = <_io.TextIOWrapper name='run.log' mode='w' encoding='UTF-8'> +outname = phb +press = 1.0 +progname = dice +randominit = first +temp = 300.0 +title = Diceplayer run +upbuf = 360 + +------------------------------------------------------------------------------------------ + GAUSSIAN variables being used in this run: +------------------------------------------------------------------------------------------ + +chgmult = 0 1 +keywords = freq=intmodes +level = MP2/aug-cc-pVDZ +pop = chelpg +qmprog = g16 + + +========================================================================================== + +Program dice found at /usr/local/bin/dice +Program g16 found at /usr/local/g16/g16 +Program formchk found at /usr/local/g16/formchk + +========================================================================================== + Potential parameters from file phb.ljc: +------------------------------------------------------------------------------------------ + +Combination rule: * +Types of molecules: 2 + +12 atoms in molecule type 1: +--------------------------------------------------------------------------------- +Lbl AN X Y Z Charge Epsilon Sigma Mass +--------------------------------------------------------------------------------- +1 6 0.00000 1.40000 0.00000 0.000000 0.11000 3.7500 12.0110 +1 6 1.21244 0.70000 0.00000 0.000000 0.11000 3.7500 12.0110 +1 6 1.21244 -0.70000 0.00000 0.000000 0.11000 3.7500 12.0110 +1 6 0.00000 -1.40000 0.00000 0.000000 0.11000 3.7500 12.0110 +1 6 -1.21244 -0.70000 0.00000 0.000000 0.11000 3.7500 12.0110 +1 6 -1.21244 0.70000 0.00000 0.000000 0.11000 3.7500 12.0110 +2 1 0.00000 2.48810 0.00000 0.000000 0.00000 0.0000 1.0079 +2 1 2.15467 1.24400 0.00000 0.000000 0.00000 0.0000 1.0079 +2 1 2.15467 -1.24400 0.00000 0.000000 0.00000 0.0000 1.0079 +2 1 0.00000 -2.48810 0.00000 0.000000 0.00000 0.0000 1.0079 +2 1 -2.15467 -1.24400 0.00000 0.000000 0.00000 0.0000 1.0079 +2 1 -2.15467 1.24400 0.00000 0.000000 0.00000 0.0000 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 10 -0.02420 -1.61760 0.00263 -0.115000 0.07000 3.5500 20.1800 +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 - BENZENO: + + Center of mass = ( 0.0000 , -0.0000 , 0.0000 ) + Moments of inertia = 8.934187E+01 8.934282E+01 1.786847E+02 + Major principal axis = ( 0.000000 , 1.000000 , 0.000000 ) + Inter principal axis = ( 1.000000 , 0.000000 , 0.000000 ) + Minor principal axis = ( 0.000000 , 0.000000 , 1.000000 ) + Characteristic lengths = ( 4.31 , 4.98 , 0.00 ) + Total mass = 78.11 au + Total charge = 0.0000 e + Dipole moment = ( 0.0000 , 0.0000 , 0.0000 ) Total = 0.0000 Debye + + Translating and rotating molecule to standard orientation... Done + + New values: + Center of mass = ( 0.0000 , -0.0000 , 0.0000 ) + Moments of inertia = 8.934187E+01 8.934282E+01 1.786847E+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 = ( 4.98 , 4.31 , 0.00 ) + Total mass = 78.11 au + Total charge = 0.0000 e + Dipole moment = ( 0.0000 , 0.0000 , 0.0000 ) Total = 0.0000 Debye + + +Molecule type 2 - PLACEHOLDER: + + Center of mass = ( 1.3581 , -1.1728 , 0.0026 ) + Moments of inertia = 1.506334E+02 3.060213E+02 4.535775E+02 + Major principal axis = ( 0.879376 , -0.476127 , -0.000001 ) + Inter principal axis = ( 0.476127 , 0.879376 , 0.000001 ) + Minor principal axis = ( 0.000000 , -0.000002 , 1.000000 ) + Characteristic lengths = ( 5.74 , 5.26 , 1.51 ) + Total mass = 132.38 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 = 1.506334E+02 3.060213E+02 4.535775E+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 = ( 5.63 , 4.95 , 1.51 ) + Total mass = 132.38 au + Total charge = -0.0000 e + Dipole moment = ( 1.9725 , 1.2491 , -0.0000 ) Total = 2.3347 Debye + +========================================================================================== + +Starting the iterative process. + +------------------------------------------------------------------------------------------ + Step # 1 +------------------------------------------------------------------------------------------ + +Simulation process simfiles/step01/p01 initiated with pid 29435 +p01> NVT thermalization finished (from random configuration) on 21 Feb 2022 at 13:19:54 +Simulation process simfiles/step01/p02 initiated with pid 29436 +p02> NVT thermalization finished (from random configuration) on 21 Feb 2022 at 13:19:54 +Simulation process simfiles/step01/p03 initiated with pid 29437 +p03> NVT thermalization finished (from random configuration) on 21 Feb 2022 at 13:19:54 +Simulation process simfiles/step01/p04 initiated with pid 29438 +p04> NVT thermalization finished (from random configuration) on 21 Feb 2022 at 13:19:54 diff --git a/run.log.backup b/run.log.backup new file mode 100644 index 0000000..cd81c45 --- /dev/null +++ b/run.log.backup @@ -0,0 +1,169 @@ +########################################################################################## +############# Welcome to DICEPLAYER version 1.0 ############# +########################################################################################## + +Your python version is 3.8.12 | packaged by conda-forge | (default, Oct 12 2021, 21:57:06) +[GCC 9.4.0] + +Program started on Monday, 21 Feb 2022 at 13:19:18 + +Environment variables: +OMP_STACKSIZE = Not set + +========================================================================================== + CONTROL variables being used in this run: +------------------------------------------------------------------------------------------ + +altsteps = 20000 +freq = no +ghosts = no +initcyc = 1 +lps = no +maxcyc = 3 +maxstep = 0.3 +nprocs = 4 +opt = no +qmprog = g16 +readhessian = no +switchcyc = 3 +tol_factor = 1.2 +vdwforces = no + +------------------------------------------------------------------------------------------ + DICE variables being used in this run: +------------------------------------------------------------------------------------------ + +combrule = * +dens = 0.75 +infile = <_io.TextIOWrapper name='control.in' mode='r' encoding='UTF-8'> +isave = 1000 +ljname = phb.ljc +ncores = 3 +nmol = 1 50 +nstep = 20000 20000 +outfile = <_io.TextIOWrapper name='run.log' mode='w' encoding='UTF-8'> +outname = phb +press = 1.0 +progname = dice +randominit = first +temp = 300.0 +title = Diceplayer run +upbuf = 360 + +------------------------------------------------------------------------------------------ + GAUSSIAN variables being used in this run: +------------------------------------------------------------------------------------------ + +chgmult = 0 1 +keywords = freq=intmodes +level = MP2/aug-cc-pVDZ +pop = chelpg +qmprog = g16 + + +========================================================================================== + +Program dice found at /usr/local/bin/dice +Program g16 found at /usr/local/g16/g16 +Program formchk found at /usr/local/g16/formchk + +========================================================================================== + Potential parameters from file phb.ljc: +------------------------------------------------------------------------------------------ + +Combination rule: * +Types of molecules: 2 + +12 atoms in molecule type 1: +--------------------------------------------------------------------------------- +Lbl AN X Y Z Charge Epsilon Sigma Mass +--------------------------------------------------------------------------------- +1 6 0.00000 1.40000 0.00000 0.000000 0.11000 3.7500 12.0110 +1 6 1.21244 0.70000 0.00000 0.000000 0.11000 3.7500 12.0110 +1 6 1.21244 -0.70000 0.00000 0.000000 0.11000 3.7500 12.0110 +1 6 0.00000 -1.40000 0.00000 0.000000 0.11000 3.7500 12.0110 +1 6 -1.21244 -0.70000 0.00000 0.000000 0.11000 3.7500 12.0110 +1 6 -1.21244 0.70000 0.00000 0.000000 0.11000 3.7500 12.0110 +2 1 0.00000 2.48810 0.00000 0.000000 0.00000 0.0000 1.0079 +2 1 2.15467 1.24400 0.00000 0.000000 0.00000 0.0000 1.0079 +2 1 2.15467 -1.24400 0.00000 0.000000 0.00000 0.0000 1.0079 +2 1 0.00000 -2.48810 0.00000 0.000000 0.00000 0.0000 1.0079 +2 1 -2.15467 -1.24400 0.00000 0.000000 0.00000 0.0000 1.0079 +2 1 -2.15467 1.24400 0.00000 0.000000 0.00000 0.0000 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 10 -0.02420 -1.61760 0.00263 -0.115000 0.07000 3.5500 20.1800 +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 - BENZENO: + + Center of mass = ( 0.0000 , -0.0000 , 0.0000 ) + Moments of inertia = 8.934187E+01 8.934282E+01 1.786847E+02 + Major principal axis = ( 0.000000 , 1.000000 , 0.000000 ) + Inter principal axis = ( 1.000000 , 0.000000 , 0.000000 ) + Minor principal axis = ( 0.000000 , 0.000000 , 1.000000 ) + Characteristic lengths = ( 4.31 , 4.98 , 0.00 ) + Total mass = 78.11 au + Total charge = 0.0000 e + Dipole moment = ( 0.0000 , 0.0000 , 0.0000 ) Total = 0.0000 Debye + + Translating and rotating molecule to standard orientation... Done + + New values: + Center of mass = ( 0.0000 , -0.0000 , 0.0000 ) + Moments of inertia = 8.934187E+01 8.934282E+01 1.786847E+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 = ( 4.98 , 4.31 , 0.00 ) + Total mass = 78.11 au + Total charge = 0.0000 e + Dipole moment = ( 0.0000 , 0.0000 , 0.0000 ) Total = 0.0000 Debye + + +Molecule type 2 - PLACEHOLDER: + + Center of mass = ( 1.3581 , -1.1728 , 0.0026 ) + Moments of inertia = 1.506334E+02 3.060213E+02 4.535775E+02 + Major principal axis = ( 0.879376 , -0.476127 , -0.000001 ) + Inter principal axis = ( 0.476127 , 0.879376 , 0.000001 ) + Minor principal axis = ( 0.000000 , -0.000002 , 1.000000 ) + Characteristic lengths = ( 5.74 , 5.26 , 1.51 ) + Total mass = 132.38 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 = 1.506334E+02 3.060213E+02 4.535775E+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 = ( 5.63 , 4.95 , 1.51 ) + Total mass = 132.38 au + Total charge = -0.0000 e + Dipole moment = ( 1.9725 , 1.2491 , -0.0000 ) Total = 2.3347 Debye + +========================================================================================== diff --git a/setup.py b/setup.py new file mode 100644 index 0000000..12466a4 --- /dev/null +++ b/setup.py @@ -0,0 +1,17 @@ +import sys +from cx_Freeze import setup, Executable + +# Dependencies are automatically detected, but it might need fine tuning. +# "packages": ["os"] is used as example only +build_exe_options = {"packages": ["os","setproctitle","nomkl","numpy"], + "bin_includes": ["/usr/bin/python3"], + "excludes": ["tkinter"], + "optimize": 0} + +name = "diceplayer" + +setup( + name = name, + version = "0.1", + executables = [Executable("diceplayer/__main__.py", target_name=name)] +) \ No newline at end of file