removed path requirement to program.py, periodic_table.csv

bicrystal/bicrystal

@@ -2,12 +2,10 @@
 
 rm -f number_of_atoms unitcell body outfile heading heading_nat atoms sorted_atoms k_points
 
-t1=$(whereis program.py | awk '{print $2}')
-t2=$(whereis program.py | awk '{print $2}' | sed -r 's/.{10}$//')
-echo $t2 > workspace
-python $t1 2>&1 | tee outfile
-rm -f workspace
+# execute python script for bicrystal
+python program.py 2>&1 | tee outfile
 
+# postprocess the results and prepare output file
 echo "Would you like to write Espresso file?[Y/n]"
 
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bicrystal/program.py

@@ -1,5 +1,3 @@
-#!/bin/python3
-
 # PROGRAM: BiCRYSTAL
 
 # VERSION: 1.0.8
@@ -8,11 +6,6 @@
 
 # AUTHOR: T. Kabengele, Johnson Chemistry Group, Dalhousie University
 
-# REQUIREMENTS:
-# Python "crystals" package must be installed on your system
-# Install via: pip install crystals
-# Alternative install: conda install -c conda-forge crystals
-
 #********************************************************************************************************
 
 # INITIALIZATION
@@ -336,12 +329,11 @@ def bulk(my_crystal):
 
 # reading csv with elements from workspace
 # i.e. directory where you installed bicrystal
-with open('workspace') as f:
+with open('program.py') as f:
     line = f.readline()
 program_directory = str(line).rstrip("\n")
-dir1 = os.path.join("" +program_directory+"", 'periodic_table.csv')
 colnames = ['number', 'symbol']
-periodic_table = pandas.read_csv(dir1, usecols=colnames)
+periodic_table = pandas.read_csv('periodic_table.csv', usecols=colnames)
 number = periodic_table.number.tolist()
 symbol = periodic_table.symbol.tolist()