Tracking Ticket for Merging My Changes

README.md

@@ -1,3 +1,11 @@
-# mosdef_cp2k_writer
+# cssi_cp2k
 
-This is an input file writer conducting molecular dynamics and Monte Carlo simulations in CP2K. For more information please visit link_to_RTD.
+More information coming soon.
+Make a `mosdef36` conda environment:
+
+```bash
+conda create -n mosdef36 -c mosdef -c conda-forge -c omnia python=3.6 mbuild foyer signac signac-flow pandas
+conda activate mosdef36
+conda install -c conda-forge openbabel  
+pip install unyt
+```

docs/requirements.txt

@@ -69,4 +69,3 @@ traitlets==4.3.3
 unyt==2.7.2
 webencodings==0.5.1
 zipp==3.1.0
-ele=0.1.0

mosdef_cp2k_writer/classes/ACC.py

@@ -1,5 +1,5 @@
 import datetime
-import mosdef_cp2k_writer.utilities
+from mosdef_cp2k_writer.utilities import test_instance as ti
 
 
 class ACC:
@@ -136,7 +136,7 @@ def AVOID_AFTER_BUSY(self, val):
 
     @BINNING_BINSIZE.setter
     def BINNING_BINSIZE(self, val):
-        if utilities.is_positive_integer(val):
+        if ti.is_positive_integer(val):
             self.__changeLog.append(
                 {
                     "Date": datetime.datetime.now(),
@@ -179,7 +179,7 @@ def BINNING_BINSIZE(self, val):
 
     @BINNING_NBINS.setter
     def BINNING_NBINS(self, val):
-        if utilities.is_positive_integer(val):
+        if ti.is_positive_integer(val):
             self.__changeLog.append(
                 {
                     "Date": datetime.datetime.now(),
@@ -222,7 +222,7 @@ def BINNING_NBINS(self, val):
 
     @MIN_FLOP_PROCESS.setter
     def MIN_FLOP_PROCESS(self, val):
-        if utilities.is_integer(val):
+        if ti.is_integer(val):
             self.__changeLog.append(
                 {
                     "Date": datetime.datetime.now(),
@@ -265,7 +265,7 @@ def MIN_FLOP_PROCESS(self, val):
 
     @POSTERIOR_BUFFERS.setter
     def POSTERIOR_BUFFERS(self, val):
-        if utilities.is_positive_integer(val):
+        if ti.is_positive_integer(val):
             self.__changeLog.append(
                 {
                     "Date": datetime.datetime.now(),
@@ -310,7 +310,7 @@ def POSTERIOR_BUFFERS(self, val):
 
     @PRIORITY_BUFFERS.setter
     def PRIORITY_BUFFERS(self, val):
-        if utilities.is_positive_integer(val):
+        if ti.is_positive_integer(val):
             self.__changeLog.append(
                 {
                     "Date": datetime.datetime.now(),
@@ -355,7 +355,7 @@ def PRIORITY_BUFFERS(self, val):
 
     @PRIORITY_STREAMS.setter
     def PRIORITY_STREAMS(self, val):
-        if utilities.is_positive_integer(val):
+        if ti.is_positive_integer(val):
             self.__changeLog.append(
                 {
                     "Date": datetime.datetime.now(),

mosdef_cp2k_writer/classes/AVBMC.py

@@ -1,10 +1,10 @@
 import datetime
-import mosdef_cp2k_writer.utilities as utilities
+from mosdef_cp2k_writer.utilities import test_instance as ti
 
 
 def _validate_AVBMC_ATOM(val, errorLog=[]):
 
-    if utilities.is_list_of_integers(val) or (val is None):
+    if ti.is_list_of_integers(val) or (val is None):
         return val
     else:
         errorMessage = (
@@ -26,7 +26,7 @@ def _validate_AVBMC_ATOM(val, errorLog=[]):
 
 def _validate_AVBMC_RMAX(val, errorLog=[]):
 
-    if utilities.is_list_of_numbers(val) or (val is None):
+    if ti.is_list_of_numbers(val) or (val is None):
         return val
     else:
         errorMessage = (
@@ -48,7 +48,7 @@ def _validate_AVBMC_RMAX(val, errorLog=[]):
 
 def _validate_AVBMC_RMIN(val, errorLog=[]):
 
-    if utilities.is_list_of_numbers(val) or (val is None):
+    if ti.is_list_of_numbers(val) or (val is None):
         return val
     else:
         errorMessage = (
@@ -70,7 +70,7 @@ def _validate_AVBMC_RMIN(val, errorLog=[]):
 
 def _validate_PBIAS(val, errorLog=[]):
 
-    if utilities.is_list_of_numbers(val) or (val is None):
+    if ti.is_list_of_numbers(val) or (val is None):
         return val
     else:
         errorMessage = (
@@ -139,7 +139,7 @@ def location(self):
 
     @AVBMC_ATOM.setter
     def AVBMC_ATOM(self, val):
-        if utilities.is_list_of_integers(val) or val is None:
+        if ti.is_list_of_integers(val) or val is None:
             self.__changeLog.append(
                 {
                     "Date": datetime.datetime.now(),
@@ -182,7 +182,7 @@ def AVBMC_ATOM(self, val):
 
     @AVBMC_RMAX.setter
     def AVBMC_RMAX(self, val):
-        if utilities.is_list_of_numbers(val) or val is None:
+        if ti.is_list_of_numbers(val) or val is None:
             self.__changeLog.append(
                 {
                     "Date": datetime.datetime.now(),
@@ -227,7 +227,7 @@ def AVBMC_RMAX(self, val):
 
     @AVBMC_RMIN.setter
     def AVBMC_RMIN(self, val):
-        if utilities.is_list_of_numbers(val) or val is None:
+        if ti.is_list_of_numbers(val) or val is None:
             self.__changeLog.append(
                 {
                     "Date": datetime.datetime.now(),
@@ -272,7 +272,7 @@ def AVBMC_RMIN(self, val):
 
     @AVBMC_RMAX.setter
     def AVBMC_RMAX(self, val):
-        if utilities.is_list_of_numbers(val) or val is None:
+        if ti.is_list_of_numbers(val) or val is None:
             self.__changeLog.append(
                 {
                     "Date": datetime.datetime.now(),
@@ -317,7 +317,7 @@ def AVBMC_RMAX(self, val):
 
     @PBIAS.setter
     def PBIAS(self, val):
-        if utilities.is_list_of_numbers(val) or val is None:
+        if ti.is_list_of_numbers(val) or val is None:
             self.__changeLog.append(
                 {
                     "Date": datetime.datetime.now(),

mosdef_cp2k_writer/classes/AVERAGES.py

@@ -1,5 +1,5 @@
 import datetime
-import mosdef_cp2k_writer.utilities as utilities
+from mosdef_cp2k_writer.utilities import test_instance as ti
 
 BOOL_VALS = [".TRUE.", ".FALSE."]
 
@@ -31,7 +31,7 @@ def _validate_SECTION_PARAMETERS(val, errorLog=[]):
 
 def _validate_ACQUISITION_START_TIME(val, errorLog=[]):
 
-    if utilities.is_positive_number(val) or (val is None):
+    if ti.is_positive_number(val) or (val is None):
         return val
     else:
         errorMessage = "Invalid option for ACQUISITION_START_TIME: {}. Must be a positive number".format(
@@ -185,7 +185,7 @@ def SECTION_PARAMETERS(self, val):
 
     @ACQUISITION_START_TIME.setter
     def ACQUISITION_START_TIME(self, val):
-        if utilities.is_positive_number(val):
+        if ti.is_positive_number(val):
 
             self.__changeLog.append(
                 {

mosdef_cp2k_writer/classes/BAROSTAT.py

@@ -1,5 +1,5 @@
 import datetime
-import mosdef_cp2k_writer.utilities as utilities
+from mosdef_cp2k_writer.utilities import test_instance as ti
 
 
 VIRIAL_VALS = ["X", "XY", "XYZ", "XZ", "Y", "YZ", "Z"]
@@ -31,7 +31,7 @@ def _validate_virial(val, errorLog=[]):
 
 
 def _validate_pressure(val, errorLog=[]):
-    if utilities.is_number(val) or (val is None):
+    if ti.is_number(val) or (val is None):
         return val
     else:
         errorMessage = "PRESSURE must be a number."
@@ -48,7 +48,7 @@ def _validate_pressure(val, errorLog=[]):
 
 
 def _validate_temperature(val, errorLog=[]):
-    if utilities.is_number(val) or (val is None):
+    if ti.is_number(val) or (val is None):
         return val
     else:
         errorMessage = "BAROSTAT TEMPERATURE must be a number."
@@ -65,7 +65,7 @@ def _validate_temperature(val, errorLog=[]):
 
 
 def _validate_temp_tol(val, errorLog=[]):
-    if utilities.is_number(val) or (val is None):
+    if ti.is_number(val) or (val is None):
         return val
     else:
         errorMessage = "BAROSTAT TEMP_TOL must be a number."
@@ -82,7 +82,7 @@ def _validate_temp_tol(val, errorLog=[]):
 
 
 def _validate_timecon(val, errorLog=[]):
-    if utilities.is_number(val) or (val is None):
+    if ti.is_number(val) or (val is None):
         return val
     else:
         errorMessage = "BAROSTAT TIMECON must be a number."
@@ -202,7 +202,7 @@ def VIRIAL(self, val):
 
     @PRESSURE.setter
     def PRESSURE(self, val):
-        if utilities.is_number(val):
+        if ti.is_number(val):
             self.__changeLog.append(
                 {
                     "Date": datetime.datetime.now(),
@@ -243,7 +243,7 @@ def PRESSURE(self, val):
 
     @TEMPERATURE.setter
     def TEMPERATURE(self, val):
-        if utilities.is_number(val):
+        if ti.is_number(val):
             self.__changeLog.append(
                 {
                     "Date": datetime.datetime.now(),
@@ -284,7 +284,7 @@ def TEMPERATURE(self, val):
 
     @TEMP_TOL.setter
     def TEMP_TOL(self, val):
-        if utilities.is_number(val):
+        if ti.is_number(val):
             self.__changeLog.append(
                 {
                     "Date": datetime.datetime.now(),
@@ -325,7 +325,7 @@ def TEMP_TOL(self, val):
 
     @TIMECON.setter
     def TIMECON(self, val):
-        if utilities.is_number(val):
+        if ti.is_number(val):
             self.__changeLog.append(
                 {
                     "Date": datetime.datetime.now(),

mosdef_cp2k_writer/classes/BOX_DISPLACEMENTS.py

@@ -1,10 +1,10 @@
 import datetime
-import mosdef_cp2k_writer.utilities as utilities
+from mosdef_cp2k_writer.utilities import test_instance as ti
 
 
 def _validate_RMCLTRANS(val, errorLog=[]):
 
-    if val is None or utilities.is_number(val):
+    if val is None or ti.is_number(val):
 
         return val
     else:
@@ -25,7 +25,7 @@ def _validate_RMCLTRANS(val, errorLog=[]):
 
 def _validate_RMVOLUME(val, errorLog=[]):
 
-    if val is None or utilities.is_number(val):
+    if val is None or ti.is_number(val):
 
         return val
     else:
@@ -76,7 +76,7 @@ def location(self):
     @RMCLTRANS.setter
     def RMCLTRANS(self, val):
 
-        if val is None or utilities.is_number(val):
+        if val is None or ti.is_number(val):
             self.__changeLog.append(
                 {
                     "Date": datetime.datetime.now(),
@@ -120,7 +120,7 @@ def RMCLTRANS(self, val):
     @RMVOLUME.setter
     def RMVOLUME(self, val):
 
-        if val is None or utilities.is_number(val):
+        if val is None or ti.is_number(val):
             self.__changeLog.append(
                 {
                     "Date": datetime.datetime.now(),

mosdef_cp2k_writer/classes/BOX_PROBABILITIES.py

@@ -1,10 +1,10 @@
 import datetime
-import mosdef_cp2k_writer.utilities as utilities
+from mosdef_cp2k_writer.utilities import test_instance as ti
 
 
 def _validate_PMCLUS_BOX(val, errorLog=[]):
 
-    if utilities.is_number(val) or (val is None):
+    if ti.is_number(val) or (val is None):
         return val
     else:
         errorMessage = "Invalid option for PMCLUS_BOX: {}. Must be a number.".format(
@@ -24,7 +24,7 @@ def _validate_PMCLUS_BOX(val, errorLog=[]):
 
 def _validate_PMHMC_BOX(val, errorLog=[]):
 
-    if utilities.is_number(val) or (val is None):
+    if ti.is_number(val) or (val is None):
         return val
     else:
         errorMessage = "Invalid option for PMHMC_BOX: {}. Must be a number.".format(val)
@@ -42,7 +42,7 @@ def _validate_PMHMC_BOX(val, errorLog=[]):
 
 def _validate_PMVOL_BOX(val, errorLog=[]):
 
-    if utilities.is_number(val) or (val is None):
+    if ti.is_number(val) or (val is None):
         return val
     else:
         errorMessage = "Invalid option for PMVOL_BOX: {}. Must be a number.".format(val)
@@ -103,7 +103,7 @@ def location(self):
     @PMCLUS_BOX.setter
     def PMCLUS_BOX(self, val):
 
-        if utilities.is_number(val) or val is None:
+        if ti.is_number(val) or val is None:
             self.__changeLog.append(
                 {
                     "Date": datetime.datetime.now(),
@@ -147,7 +147,7 @@ def PMCLUS_BOX(self, val):
     @PMHMC_BOX.setter
     def PMHMC_BOX(self, val):
 
-        if utilities.is_number(val) or val is None:
+        if ti.is_number(val) or val is None:
             self.__changeLog.append(
                 {
                     "Date": datetime.datetime.now(),
@@ -191,7 +191,7 @@ def PMHMC_BOX(self, val):
     @PMVOL_BOX.setter
     def PMVOL_BOX(self, val):
 
-        if utilities.is_number(val) or val is None:
+        if ti.is_number(val) or val is None:
             self.__changeLog.append(
                 {
                     "Date": datetime.datetime.now(),

mosdef_cp2k_writer/classes/CELL.py

@@ -1,5 +1,5 @@
 import datetime
-import mosdef_cp2k_writer.utilities as utilities
+from mosdef_cp2k_writer.utilities import test_instance as ti
 from mosdef_cp2k_writer.classes import CELL_REF
 
 BOOL_VALS = [".TRUE.", ".FALSE."]

mosdef_cp2k_writer/classes/CELL_REF.py

@@ -1,5 +1,5 @@
 import datetime
-import mosdef_cp2k_writer.utilities as utilities
+from mosdef_cp2k_writer.utilities import test_instance as ti
 
 
 BOOL_VALS = [".TRUE.", ".FALSE."]