Read Potentials and Initial Testing

diceplayer/shared/utils/dataclass_protocol.py

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+from typing import runtime_checkable, Protocol
+
+
+@runtime_checkable
+class Dataclass(Protocol):
+    __dataclass_fields__: dict

diceplayer/shared/utils/misc.py

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+import gzip
+import os
+import shutil
+import sys
+import time
+from typing import Final
+
+#######################################  constants  ######################################
+
+
+BOHR2ANG: Final[float] = 0.52917721092
+ANG2BOHR: Final[float] = 1 / BOHR2ANG
+
+
+#######################################  functions  ######################################
+
+def weekday_date_time():
+    return time.strftime("%A, %d %b %Y at %H:%M:%S")
+
+
+def date_time():
+    return time.strftime("%d %b %Y at %H:%M:%S")
+
+
+def compress_files_1mb(path):
+    working_dir = os.getcwd()
+    os.chdir(path)
+
+    files = filter(os.path.isfile, os.listdir(os.curdir))
+    for file in files:
+        if os.path.getsize(file) > 1024 * 1024:  ## If bigger than 1MB
+            filegz = file + ".gz"
+            try:
+                with open(file, 'rb') as f_in:
+                    with gzip.open(filegz, 'wb') as f_out:
+                        shutil.copyfileobj(f_in, f_out)
+            except:
+                sys.exit("Error: cannot compress file {}".format(file))
+
+    os.chdir(working_dir)
+
+    return
+
+
+def make_step_dir(cycle):
+    sim_dir = "simfiles"
+    step_dir = "step{:02d}".format(cycle)
+    path = sim_dir + os.sep + step_dir
+    if os.path.exists(path):
+        sys.exit("Error: a file or directory {} already exists".format(step_dir))
+    try:
+        os.makedirs(path)
+    except:
+        sys.exit("Error: cannot make directory {}".format(step_dir))
+
+
+def make_qm_dir(cycle):
+    sim_dir = "simfiles"
+    step_dir = "step{:02d}".format(cycle)
+    path = sim_dir + os.sep + step_dir + os.sep + "qm"
+    try:
+        os.makedirs(path)
+    except:
+        sys.exit("Error: cannot make directory {}".format(path))

diceplayer/shared/utils/ptable.py

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+####  Label used in Dice for a ghost atom
+dice_ghost_label = "Xx"
+
+####  Tuple of atom symbols
+atomsymb = ( "00",
+
+"H ",                                                                                "He",
+"Li","Be",                                                  "B ","C ","N ","O ","F ","Ne",
+"Na","Mg",                                                  "Al","Si","P ","S ","Cl","Ar",
+"K ","Ca","Sc","Ti","V ","Cr","Mn","Fe","Co","Ni","Cu","Zn","Ga","Ge","As","Se","Br","Kr",
+"Rb","Sr","Y ","Zr","Nb","Mo","Tc","Ru","Rh","Pd","Ag","Cd","In","Sn","Sb","Te","I ","Xe",
+"Cs","Ba",
+          "La","Ce","Pr","Nd","Pm","Sm","Eu","Gd","Tb","Dy","Ho","Er","Tm","Yb","Lu",
+               "Hf","Ta","W ","Re","Os","Ir","Pt","Au","Hg","Ti","Pb","Bi","Po","At","Rn",
+"Fr","Ra",
+          "Ac","Th","Pa","U ","Np","Pu","Am","Cm","Bk","Cf","Es","Fm","Md","No","Lr",
+               dice_ghost_label )
+               
+####  Tuple of atom masses  
+atommass = ( 0.0,
+
+1.0079, 													                                                           4.0026,
+6.9410,9.0122,									                                    10.811,12.011,14.007,15.999,18.998,20.180,
+22.990,24.305,									                                    26.982,28.086,30.974,32.065,35.453,39.948,
+39.098,40.078,44.956,47.867,50.942,51.996,54.938,55.845,58.933,58.693,63.546,65.409,69.723,72.640,74.922,78.960,79.904,83.798,
+85.468,87.620,88.906,91.224,92.906,95.940,98.000,101.07,102.91,106.42,107.87,112.41,114.82,118.71,121.76,127.60,126.90,131.29,
+132.91,137.33,
+              138.91,140.12,140.91,144.24,145.00,150.36,151.96,157.25,158.93,162.50,164.93,167.26,168.93,173.04,174.97,
+                     178.49,180.95,183.84,186.21,190.23,192.22,195.08,196.97,200.59,204.38,207.20,208.98,209.00,210.00,222.00,
+223.00,226.00,
+              227.00,232.04,231.04,238.03,237.00,244.00,243.00,247.00,247.00,251.00,252.00,257.00,258.00,259.00,262.00,
+                     0.000 )
+
+####  Number of the ghost atom
+ghost_number = len(atomsymb) - 1

diceplayer/shared/utils/validations.py

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+def NotNull(requiredArgs=[]):
+    def _NotNull(function):
+        def wrapper(*args, **kwargs):
+            for arg in requiredArgs:
+                try:
+                    assert (
+                        kwargs.get(arg) is not None
+                    ), "Invalid Config File. Keyword {} is required".format(arg)
+                except AssertionError as err:
+                    print(err)
+            return function(*args, **kwargs)
+
+        return wrapper
+
+    return _NotNull