removed references to lammps in develop

shirtsgroup · Jan 21, 2015 · 4bd0e4d · 4bd0e4d
1 parent 0f80793
commit 4bd0e4d
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Showing 2 changed files with 8 additions and 37 deletions.
diff --git a/intermol/convert.py b/intermol/convert.py
@@ -7,7 +7,6 @@
 import numpy as np
 
 from intermol.gromacs import gromacs_driver
-from intermol.lammps import lammps_driver
 import intermol.tests
 
 
@@ -124,10 +123,6 @@ def main(args=None):
         gro_in = gro_in[0]
 
         system = gromacs_driver.read_file(top_in, gro_in, gropath)
-    elif args.get('lmp_in'):
-        lammps_file = args['lmp_in']
-        prefix = os.path.splitext(os.path.basename(lammps_file))[0]
-        system = lammps_driver.read_file(in_file=lammps_file)
     else:
         logger.error('No input file')
         sys.exit(1)
@@ -151,15 +146,6 @@ def main(args=None):
         else:
             output_status['gromacs'] = 0
 
-    if args.get('lammps'):
-        try:
-            lammps_driver.write_file('{0}.input'.format(oname), system)
-        except Exception as e:
-            logger.exception(e)
-            output_status['lammps'] = e
-        else:
-            output_status['lammps'] = 0
-
     # --------------- ENERGY EVALUATION ----------------- #
     if args.get('energy'):
         # Run control file paths.
@@ -198,21 +184,6 @@ def main(args=None):
                 e_out.append(out)
                 e_outfile.append(outfile)
 
-        if args.get('lammps') and output_status['lammps'] == 0:
-            output_type.append('lammps')
-            try:
-                out, outfile = lammps_driver.lammps_energies(
-                        '{0}.input'.format(oname), lmppath)
-            except Exception as e:
-                output_status['lammps'] = e
-                logger.exception(e)
-                e_out.append(-1)
-                e_outfile.append(-1)
-            else:
-                output_status['lammps'] = get_diff(e_in, out)
-                e_out.append(out)
-                e_outfile.append(outfile)
-
         # Display energy comparison results.
         out = ['InterMol Conversion Energy Comparison Results','']
         out.append('{0} input energy file: {1}'.format(input_type, e_infile))

diff --git a/intermol/forces/convert_dihedrals.py b/intermol/forces/convert_dihedrals.py
@@ -14,14 +14,14 @@ def convert_dihedral_from_proper_to_trig(p):
     multiplicity = p['multiplicity']
     zu = 0*k.unit
     fcs = {
-        'phi' : p['phi'],
-        'fc0' : k,
-        'fc1' : zu,
-        'fc2' : zu,
-        'fc3' : zu,
-        'fc4' : zu,
-        'fc5' : zu,
-        'fc6' : zu
+        'phi': p['phi'],
+        'fc0': k,
+        'fc1': zu,
+        'fc2': zu,
+        'fc3': zu,
+        'fc4': zu,
+        'fc5': zu,
+        'fc6': zu
         }
 
     k # which force constant is nonzero because of the multiplicity?