Adding stable dependencies to project

Pipfile

@@ -0,0 +1,23 @@
+[[source]]
+url = "https://pypi.org/simple"
+verify_ssl = true
+name = "pypi"
+
+[packages]
+numpy = "*"
+pyinstaller = "*"
+pyinstall = "*"
+argparse = "*"
+typing = "*"
+nptyping = "*"
+"subprocess.run" = "*"
+multiprocess = "*"
+setproctitle = "*"
+textwrap3 = "*"
+pathlib = "*"
+gzip-utils = "*"
+
+[dev-packages]
+
+[requires]
+python_version = "3.8"

diceplayer/DPpack/Player.py

@@ -612,17 +612,13 @@ class Player:
 
         self.gaussian.reset()
 
-    # I still have to talk with Herbet about this function
     def populate_asec_vdw(self, cycle):
 
         # Both asec_charges and vdw_meanfield will utilize the Molecule() class and Atoms() with some None elements
 
         asec_charges = Molecule(
             "ASEC_CHARGES"
-        )  # (lbl=None, na=None, rx, ry, rz, chg, eps=None, sig=None)
-        # vdw_meanfield = (
-        #     Molecule()
-        # )  # (lbl=None, na=None, rx, ry, rz, chg=None, eps, sig)
+        )
 
         if self.dice.nstep[-1] % self.dice.isave == 0:
             nconfigs = round(self.dice.nstep[-1] / self.dice.isave)
@@ -632,11 +628,6 @@ class Player:
         norm_factor = nconfigs * self.nprocs
 
         nsitesref = len(self.system.molecule[0].atom)
-        # nsitesref = (
-        #     len(self.system.molecule[0].atom)
-        #     + len(self.system.molecule[0].ghost_atoms)
-        #     + len(self.system.molecule[0].lp_atoms)
-        # )
 
         nsites_total = self.dice.nmol[0] * nsitesref
         for i in range(1, len(self.dice.nmol)):
@@ -647,9 +638,8 @@ class Player:
 
         for proc in range(1, self.nprocs + 1):  # Run over folders
 
-            simdir = "simfiles"
             path = (
-                simdir
+                "simfiles"
                 + os.sep
                 + "step{:02d}".format(cycle)
                 + os.sep
@@ -682,19 +672,18 @@ class Player:
                     )
                 )
 
-                # Skip the first (reference) molecule
                 xyzfile = xyzfile[nsitesref:]
                 mol_count = 0
-                for type in range(len(self.dice.nmol)):  # Run over types of molecules
+                for type in range(len(self.dice.nmol)):
 
                     if type == 0:
                         nmols = self.dice.nmol[0] - 1
                     else:
                         nmols = self.dice.nmol[type]
 
-                    for mol in range(nmols):  # Run over molecules of each type
+                    for mol in range(nmols):
 
-                        new_molecule = Molecule(self.system.molecule[type].molname)
+                        new_molecule = Molecule(self.system.molecule[type])
                         # Run over sites of each molecule
                         for site in range(len(self.system.molecule[types].atom)):
 

diceplayer/__main__.py

@@ -1,5 +1,3 @@
-#!/usr/bin/python3
-
 import argparse
 import os
 import pickle
@@ -20,24 +18,24 @@ if __name__ == "__main__":
 
     parser = argparse.ArgumentParser(prog="Diceplayer")
     parser.add_argument(
-        "--continue", dest="opt_continue", default=False, action="store_true"
+        "-c", "--continue", dest="opt_continue", default=False, action="store_true"
     )
     parser.add_argument(
-        "--version", action="version", version="diceplayer-" + __VERSION
+        "-v", "--version", action="version", version="diceplayer-" + __VERSION
     )
     parser.add_argument(
-        "-i",
+        "-i", "--input",
         dest="infile",
         default="control.yml",
         metavar="INFILE",
-        help="input file of diceplayer [default = control.in]",
+        help="input file of diceplayer [default = control.in]"
     )
     parser.add_argument(
-        "-o",
+        "-o", "--output",
         dest="outfile",
         default="run.log",
         metavar="OUTFILE",
-        help="output file of diceplayer [default = run.log]",
+        help="output file of diceplayer [default = run.log]"
     )
     ## Study the option of a parameter for continuing the last process via data from control.in and run.log files