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Translation of Gaussian Processes and Step Calculations Fixes

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This commit temporarily uses Gaussian Heassian for step calculations, fixes fchk file reading, fixes step calculation, fixes log file and geoms formation. Also this commit adds type hinting to improve and facilitate the program development.
This commit is contained in:
Vitor Hideyoshi
2021-12-09 00:11:35 +00:00
parent 2a4e9eff0c
commit 926ffc5c6b
12 changed files with 515 additions and 3218 deletions
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212
run.log
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@@ -1,212 +0,0 @@
##########################################################################################
############# Welcome to DICEPLAYER version 1.0 #############
##########################################################################################
Your python version is 3.6.9 (default, Jan 26 2021, 15:33:00)
[GCC 8.4.0]
Program started on Friday, 03 Dec 2021 at 21:20:24
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 = yes
qmprog = g16
readhessian = no
switchcyc = 3
tol_factor = 1.2
vdwforces = no
------------------------------------------------------------------------------------------
DICE variables being used in this run:
------------------------------------------------------------------------------------------
combrule = *
dens = 0.75
isave = 1000
ljname = phb.ljc
ncores = 3
nmol = 1 50
nstep = 20000 20000
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
level = MP2/aug-cc-pVTZ
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
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 6 0.67589 -0.40522 0.00264 0.150000 0.07000 3.5500 12.0110
1 6 -0.02420 -1.61760 0.00263 -0.115000 0.07000 3.5500 12.0110
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 - PHENOL_BLUE:
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 - PLACEHOLDER:
Center of mass = ( 1.5639 , -1.2534 , 0.0026 )
Moments of inertia = 1.394830E+02 2.777126E+02 4.141185E+02
Major principal axis = ( 0.865900 , -0.500217 , -0.000001 )
Inter principal axis = ( 0.500217 , 0.865900 , 0.000001 )
Minor principal axis = ( 0.000000 , -0.000002 , 1.000000 )
Characteristic lengths = ( 5.74 , 5.26 , 1.51 )
Total mass = 108.14 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 = 1.394830E+02 2.777126E+02 4.141185E+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 = ( 5.65 , 4.95 , 1.51 )
Total mass = 108.14 au
Total charge = -0.0000 e
Dipole moment = ( 1.9373 , 1.3031 , -0.0000 ) Total = 2.3347 Debye
==========================================================================================
Starting the iterative process.
------------------------------------------------------------------------------------------
Step # 1
------------------------------------------------------------------------------------------
Simulation process simfiles/step01/p01 initiated with pid 8024
p01> NVT thermalization finished (from random configuration) on 03 Dec 2021 at 21:20:24
Simulation process simfiles/step01/p03 initiated with pid 8026
p03> NVT thermalization finished (from random configuration) on 03 Dec 2021 at 21:20:24
Simulation process simfiles/step01/p02 initiated with pid 8025
p02> NVT thermalization finished (from random configuration) on 03 Dec 2021 at 21:20:24
Simulation process simfiles/step01/p04 initiated with pid 8027
p04> NVT thermalization finished (from random configuration) on 03 Dec 2021 at 21:20:24
p02> NVT production initiated on 03 Dec 2021 at 21:21:22
p04> NVT production initiated on 03 Dec 2021 at 21:21:23
p03> NVT production initiated on 03 Dec 2021 at 21:21:23
p01> NVT production initiated on 03 Dec 2021 at 21:21:27
p03> ----- NVT production finished on 03 Dec 2021 at 21:22:35
p04> ----- NVT production finished on 03 Dec 2021 at 21:22:36
p02> ----- NVT production finished on 03 Dec 2021 at 21:22:36
p01> ----- NVT production finished on 03 Dec 2021 at 21:22:39
+----------------------------------------------------------------------------------------+
Calculation of forces initiated with Gaussian on 03 Dec 2021 at 21:22:39