Initial Translation of Gaussian Processes and Packaging of DicePlayer python module
This commit adds the methods that were present in the Gaussian.py file into the SetGlobals.py file and packages the program into a diceplayer module so it can be ran using 'python3 -m diceplayer' Signed-off-by: Vitor Hideyoshi <vitor.h.n.batista@gmail.com>
This commit is contained in:
110
run.log
110
run.log
@@ -5,7 +5,7 @@
|
||||
Your python version is 3.6.9 (default, Jan 26 2021, 15:33:00)
|
||||
[GCC 8.4.0]
|
||||
|
||||
Program started on Saturday, 20 Nov 2021 at 14:52:20
|
||||
Program started on Friday, 03 Dec 2021 at 21:20:24
|
||||
|
||||
Environment variables:
|
||||
OMP_STACKSIZE = Not set
|
||||
@@ -22,7 +22,7 @@ lps = no
|
||||
maxcyc = 3
|
||||
maxstep = 0.3
|
||||
nprocs = 4
|
||||
opt = no
|
||||
opt = yes
|
||||
qmprog = g16
|
||||
readhessian = no
|
||||
switchcyc = 3
|
||||
@@ -39,7 +39,7 @@ isave = 1000
|
||||
ljname = phb.ljc
|
||||
ncores = 3
|
||||
nmol = 1 50
|
||||
nstep = 40000 60000 50000
|
||||
nstep = 20000 20000
|
||||
outname = phb
|
||||
press = 1.0
|
||||
progname = dice
|
||||
@@ -115,8 +115,8 @@ Lbl AN X Y Z Charge Epsilon Sigma Mass
|
||||
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
|
||||
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
|
||||
@@ -159,13 +159,13 @@ Molecule type 1 - PHENOL_BLUE:
|
||||
|
||||
Molecule type 2 - PLACEHOLDER:
|
||||
|
||||
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 )
|
||||
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 = 112.20 au
|
||||
Total mass = 108.14 au
|
||||
Total charge = -0.0000 e
|
||||
Dipole moment = ( 2.3293 , 0.1593 , -0.0000 ) Total = 2.3347 Debye
|
||||
|
||||
@@ -173,14 +173,14 @@ Molecule type 2 - PLACEHOLDER:
|
||||
|
||||
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 )
|
||||
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 = ( 5.67 , 5.13 , 1.51 )
|
||||
Total mass = 112.20 au
|
||||
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 = ( 1.7575 , 1.5369 , -0.0000 ) Total = 2.3347 Debye
|
||||
Dipole moment = ( 1.9373 , 1.3031 , -0.0000 ) Total = 2.3347 Debye
|
||||
|
||||
==========================================================================================
|
||||
|
||||
@@ -190,67 +190,23 @@ Starting the iterative process.
|
||||
Step # 1
|
||||
------------------------------------------------------------------------------------------
|
||||
|
||||
Simulation process simfiles/step01/p02 initiated with pid 15516
|
||||
p02> NVT thermalization initiated (from random configuration) on 20 Nov 2021 at 14:52:20
|
||||
Simulation process simfiles/step01/p01 initiated with pid 15515
|
||||
p01> NVT thermalization initiated (from random configuration) on 20 Nov 2021 at 14:52:20
|
||||
Simulation process simfiles/step01/p03 initiated with pid 15517
|
||||
p03> NVT thermalization initiated (from random configuration) on 20 Nov 2021 at 14:52:20
|
||||
Simulation process simfiles/step01/p04 initiated with pid 15518
|
||||
p04> NVT thermalization initiated (from random configuration) on 20 Nov 2021 at 14:52:20
|
||||
p03> NPT thermalization finished (from previous configuration) on 20 Nov 2021 at 14:54:12
|
||||
p04> NPT thermalization finished (from previous configuration) on 20 Nov 2021 at 14:54:13
|
||||
p02> NPT thermalization finished (from previous configuration) on 20 Nov 2021 at 14:54:13
|
||||
p01> NPT thermalization finished (from previous configuration) on 20 Nov 2021 at 14:54:13
|
||||
p03> NPT production initiated on 20 Nov 2021 at 14:57:16
|
||||
p02> NPT production initiated on 20 Nov 2021 at 14:57:19
|
||||
p04> NPT production initiated on 20 Nov 2021 at 14:57:20
|
||||
p01> NPT production initiated on 20 Nov 2021 at 14:57:21
|
||||
p03> ----- NPT production finished on 20 Nov 2021 at 15:00:16
|
||||
p02> ----- NPT production finished on 20 Nov 2021 at 15:00:21
|
||||
p04> ----- NPT production finished on 20 Nov 2021 at 15:00:23
|
||||
p01> ----- NPT production finished on 20 Nov 2021 at 15:00:27
|
||||
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
|
||||
|
||||
+----------------------------------------------------------------------------------------+
|
||||
Step # 2
|
||||
------------------------------------------------------------------------------------------
|
||||
|
||||
Simulation process simfiles/step02/p02 initiated with pid 15559
|
||||
p02> NPT thermalization finished (from previous configuration) on 20 Nov 2021 at 15:00:27
|
||||
Simulation process simfiles/step02/p01 initiated with pid 15558
|
||||
p01> NPT thermalization finished (from previous configuration) on 20 Nov 2021 at 15:00:27
|
||||
Simulation process simfiles/step02/p03 initiated with pid 15560
|
||||
p03> NPT thermalization finished (from previous configuration) on 20 Nov 2021 at 15:00:27
|
||||
Simulation process simfiles/step02/p04 initiated with pid 15561
|
||||
p04> NPT thermalization finished (from previous configuration) on 20 Nov 2021 at 15:00:27
|
||||
p03> NPT production initiated on 20 Nov 2021 at 15:01:30
|
||||
p01> NPT production initiated on 20 Nov 2021 at 15:01:30
|
||||
p02> NPT production initiated on 20 Nov 2021 at 15:01:31
|
||||
p04> NPT production initiated on 20 Nov 2021 at 15:01:31
|
||||
p03> ----- NPT production finished on 20 Nov 2021 at 15:04:29
|
||||
p02> ----- NPT production finished on 20 Nov 2021 at 15:04:33
|
||||
p01> ----- NPT production finished on 20 Nov 2021 at 15:04:34
|
||||
p04> ----- NPT production finished on 20 Nov 2021 at 15:04:37
|
||||
|
||||
+----------------------------------------------------------------------------------------+
|
||||
Step # 3
|
||||
------------------------------------------------------------------------------------------
|
||||
|
||||
Simulation process simfiles/step03/p01 initiated with pid 15661
|
||||
p01> NPT thermalization finished (from previous configuration) on 20 Nov 2021 at 15:04:37
|
||||
Simulation process simfiles/step03/p02 initiated with pid 15662
|
||||
p02> NPT thermalization finished (from previous configuration) on 20 Nov 2021 at 15:04:37
|
||||
Simulation process simfiles/step03/p04 initiated with pid 15664
|
||||
p04> NPT thermalization finished (from previous configuration) on 20 Nov 2021 at 15:04:37
|
||||
Simulation process simfiles/step03/p03 initiated with pid 15663
|
||||
p03> NPT thermalization finished (from previous configuration) on 20 Nov 2021 at 15:04:37
|
||||
p03> NPT production initiated on 20 Nov 2021 at 15:05:41
|
||||
p01> NPT production initiated on 20 Nov 2021 at 15:05:42
|
||||
p04> NPT production initiated on 20 Nov 2021 at 15:05:42
|
||||
p02> NPT production initiated on 20 Nov 2021 at 15:05:44
|
||||
p01> ----- NPT production finished on 20 Nov 2021 at 15:08:44
|
||||
p03> ----- NPT production finished on 20 Nov 2021 at 15:08:45
|
||||
p04> ----- NPT production finished on 20 Nov 2021 at 15:08:48
|
||||
p02> ----- NPT production finished on 20 Nov 2021 at 15:08:51
|
||||
|
||||
+----------------------------------------------------------------------------------------+
|
||||
Calculation of forces initiated with Gaussian on 03 Dec 2021 at 21:22:39
|
||||
|
||||
Reference in New Issue
Block a user