complete Alex-AMC edits and suggestions

Author: ramayo223

scripts/particle_rugosity/ReadMe.md

@@ -15,7 +15,7 @@ Using a protocol similar to that reported by [Cruz-Cabeza and colleagues](https:
 takes a crystal structure or refcode as an argument and will use the CCDC BFDH 
 morphology module to simulate the predicted particle shape. The facet hkl planes are
 then obtained and the rugosity of these planes is calculated using the [CCDC rugosity function](https://downloads.ccdc.cam.ac.uk/documentation/API/descriptive_docs/particle.html) (including a scan of 
-different off-sets from the origin to identify the minimum rugosity of that crystal 
+different offsets from the origin to identify the minimum rugosity of that crystal 
 plane). Finally, the total particle rugosity is calculated by weighted average 
 according to the facet surface areas.
 
@@ -27,7 +27,7 @@ according to the facet surface areas.
 
 ## Licensing Requirements
 
-- CSD-Core
+- CSD-Core, CSD-Particle
 
 ## Instructions on Running
 ### Linux command line
@@ -37,7 +37,7 @@ according to the facet surface areas.
 $ python particle_rugosity.py AABHTZ
 The crystal structure AABHTZ has been loaded
 Calculating particle rugosity ...
-AABHTZ particle rugosity:  1.5073781143188552
+AABHTZ particle rugosity:  1.507
 ~~~
 OR
 ~~~
@@ -60,22 +60,21 @@ C:\Program Files\CCDC\Python_API_2022\
 the last line is the folder location where you need to move the particle\_rugostiy.py file
 - now the script can be run in the CSD Python API to calculate the rugosity of any CSD entry using:
 ~~~
->>> import sys
->>> import subprocess
->>> subprocess.call([sys.executable, 'particle_rugosity.py', 'AABHTZ'])
+>>> from particle_rugosity import particle_rugosity
+>>> particle_rugosity('AABHTZ')
 The crystal structure AABHTZ has been loaded
 Calculating particle rugosity ...
-AABHTZ particle rugosity:  1.5073781143188552
+AABHTZ particle rugosity:  1.507
 ~~~
 OR
 - if you want to run your own crystal structures, make a folder (eg. rugosity_calc) in Python_API_(year), and add your
  crystal structure file to that folder
 - modify the argument to include the file path
 ~~~
->>> subprocess.call([sys.executable, 'particle_rugosity.py', 'rugosity_calc/AABHTZ.cif'])
+>>> particle_rugosity('rugosity_calc/AABHTZ.cif')
 The crystal structure rugosity_calc/AABHTZ.cif has been loaded
 Calculating particle rugosity ...
-AABHTZ particle rugosity:  1.5073781143188552
+rugosity_calc/AABHTZ.cif particle rugosity:  1.507
 ~~~
 
 ## Author

scripts/particle_rugosity/particle_rugosity.py

@@ -2,27 +2,38 @@
 # requires a CCDC license, and loading of the CSD-python miniconda environment if run from Linux command line
 
 # import ccdc modules
+import os as opsys
+import argparse
 from ccdc.io import CrystalReader
 from ccdc.particle import Surface
 from ccdc.morphology import BFDHMorphology
 
-def particle_rugosity(crystal):
+def particle_rugosity(xname):
+# xname is a string, either refcode (eg: 'AABHTZ') or filename (eg: 'AABHTZ.cif')
 # load structure, either (1) crystal structure file in working directory, or 
 # (2) CSD refcode
-    head, sep, tail = crystal.partition('.')
-    if sep == '.':
-    # agrument is crystal structure file 
-        xname = crystal
-        xtal1 = CrystalReader(xname)
-        xtal = xtal1[0]
-        xtal1.close
+    if opsys.path.isfile(xname):
+        try:
+        # agrument is crystal structure file 
+            xtal1 = CrystalReader(xname)
+            xtal = xtal1[0]
+            xtal1.close
+        except:
+            print("Error in reading crystal structure input.\nPlease enter a CSD refcode or provide the path to your crystal structure file")
+            input('Press ENTER to exit')
+            quit()
     else:
-    # agrument is a CSD refcode 
-        xname = crystal
-        xtal = CrystalReader('CSD').crystal(xname)
-
-    print(f"The crystal structure {crystal} has been loaded")
+        try:
+        # agrument is a CSD refcode 
+            xtal = CrystalReader('CSD').crystal(xname)
+        except:
+            print("Error in reading crystal structure input.\nPlease enter a CSD refcode or provide the path to your crystal structure file")
+            input('Press ENTER to exit')
+            quit()
+ 
+    print(f"The crystal structure {xname} has been loaded")
     print("Calculating particle rugosity ...")
+
 # run BFDH morphology to determine predicted particle surface area = hkl planes, and d-spacing of the planes
     morphology = BFDHMorphology(xtal)
     facets = morphology.facets
@@ -32,11 +43,13 @@ def particle_rugosity(crystal):
     facets_relA = [morphology.relative_area(mi) for mi in all_mi]
     all_d_hkl = [f.miller_indices.d_spacing for f in facets]
     num_face = len(all_d_hkl)
+    
 # generate surfaces and record rugosity, weigh by particle surface area
     w_part_rug = []
     for i in range(num_face):
         hkl = all_hkl[i]
         rug_list = []
+
         # check rugosity of crystal plane at 0, 0.25, 0.5, and 0.75 offset from origin 
         for split in range(1,5):
             os = all_d_hkl[i] / split
@@ -50,16 +63,15 @@ def particle_rugosity(crystal):
 
 # sum weighted rugosity values and print total particle rugosity
     tot_rug = sum(w_part_rug)
-    print(f'{crystal} particle rugosity: ',tot_rug)
+    print(f'{xname} particle rugosity: ',round(tot_rug, 3))
 
 # ================================
-# argument parser
-import argparse
-parser = argparse.ArgumentParser()
-parser.add_argument("input_x")
-args = parser.parse_args()
-crystal = args.input_x
+if __name__=='__main__':
+    parser = argparse.ArgumentParser()
+    parser.add_argument("input_x")
+    args = parser.parse_args()
+    crystal = args.input_x
 
-# run code
-particle_rugosity(crystal)
+    # run code
+    particle_rugosity(crystal)