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SetGlobas/MolHandling(fixes)/DicePlayer Translation

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Fixed Numerus functions in the SetGlobals file and MolHandling, translated DicePlayer and tested till, such as inertia_tensor, add_type, center_of_mass_to_origin. standard_orientation; and removed chglevel keyword

Signed-off-by: Vitor Hideyoshi <vitor.h.n.batista@gmail.com>
This commit is contained in:
Vitor Hideyoshi
2021-10-24 00:55:11 -03:00
committed by Vitor Hideyoshi
parent 316acf4761
commit 6017f272b3
5 changed files with 64 additions and 77 deletions
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32
DPpack/SetGlobals.py
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@@ -1,6 +1,7 @@
import os, sys
import shutil
import textwrap
import types
from DPpack.MolHandling import *
from DPpack.PTable import *
@@ -179,8 +180,8 @@ class Internal:
except ValueError:
sys.exit(err)
elif key in ('level', 'chglevel'):
setattr(self.gaussian, key, value[0])
elif key == 'level':
setattr(self.gaussian, key, value)
elif key in ('gmiddle', 'gbottom'):
setattr(self.gaussian, key, value[0])
@@ -243,9 +244,6 @@ class Internal:
if self.gaussian.pop != "chelpg" and (self.player.ghosts == "yes" or self.player.lps == "yes"):
sys.exit("Error: ghost atoms or lone pairs only available with 'pop = chelpg')")
if self.gaussian.chglevel == None:
self.gaussian.chglevel = self.gaussian.level
## Check only if QM program is Molcas:
# if self.player.qmprog == "molcas":
@@ -636,7 +634,7 @@ class Internal:
pass
### I still have to talk with Herbet about
def populate_asec_vdw(self, cycle):
asec_charges = [] # (rx, ry, rz, chg)
@@ -651,17 +649,17 @@ class Internal:
nsitesref = len(self.system.molecule[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])
nsites_total = self.dice.nmol[0] * nsitesref
for i in range(1, len(self.dice.nmol)):
nsites_total += self.dice.nmol[i] * len(self.system.molecule[i])
thickness = []
picked_mols = []
for proc in range(1, player['nprocs'] + 1): ## Run over folders
for proc in range(1, self.player.nprocs + 1): ## Run over folders
path = "step{:02d}".format(cycle) + os.sep + "p{:02d}".format(proc)
file = path + os.sep + dice['outname'] + ".xyz"
file = path + os.sep + self.dice.outname + ".xyz"
if not os.path.isfile(file):
sys.exit("Error: cannot find file {}".format(file))
try:
@@ -677,23 +675,23 @@ class Internal:
box = xyzfile.pop(0).split()[-3:]
box = [ float(box[0]), float(box[1]), float(box[2]) ]
sizes = sizes_of_molecule(molecules[0])
sizes = self.system.molecule[0].sizes_of_molecule()
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
for type in range(len(self.dice.nmol)): ## Run over types of molecules
if type == 0:
nmols = dice['nmol'][0] - 1
nmols = self.dice.nmol[0] - 1
else:
nmols = dice['nmol'][type]
nmols = self.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
for site in range(len(self.system.molecule[types].atoms)): ## Run over sites of each molecule
new_molecule.append({})
line = xyzfile.pop(0).split()
@@ -831,8 +829,6 @@ class Internal:
self.gmiddle = None # In each case, if a filename is given, its content will be
self.gbottom = None # inserted in the gaussian input
self.pop = "chelpg"
self.chglevel = None
self.level = None
# class Molcas: