forked from lijiext/lammps
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14269 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
parent
7189cdd80d
commit
b857237fef
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@ -185,28 +185,28 @@ def LookupBondTypes(bond_types,
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bondid = bond_ids[ie]
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(atomid1, atomid2) = bond_pairs[ie]
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if atomid1 not in atomids2types:
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raise ttree_lex.InputError('Error: atom \"'+atomid1+'\" not defined in \"Data Atoms\".\n'
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' This usually happens when the user mistypes one of the names of the\n'
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' $atoms in either a \"Data Atoms\" or \"Data Bond List\" section.\n'
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' To find out where the mistake occured, search the \n'
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' \"ttree_assignments.txt\" file for:\n'
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' \"'+atomid1+'\"\n')
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if atomid2 not in atomids2types:
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raise ttree_lex.InputError('Error: atom \"'+atomid2+'\" not defined in \"Data Atoms\".\n'
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' This usually happens when the user mistypes one of the names of the\n'
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' $atoms in either a \"Data Atoms\" or \"Data Bond List\" section.\n'
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' To find out where the mistake occured, search the \n'
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' \"ttree_assignments.txt\" file for:\n'
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' \"'+atomid2+'\"\n')
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atomtype1 = atomids2types[atomid1]
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atomtype2 = atomids2types[atomid2]
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#for n in range(0, len(typepattern_to_coefftypes)):
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for typepattern, coefftype in typepattern_to_coefftypes:
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if atomid1 not in atomids2types:
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raise ttree_lex.InputError('Error: atom \"'+atomid1+'\" not defined in \"Data Atoms\".\n'
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' This usually happens when the user mistypes one of the names of the\n'
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' $atoms in either a \"Data Atoms\" or \"Data Bond List\" section.\n'
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' To find out where the mistake occured, search the \n'
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' \"ttree_assignments.txt\" file for:\n'
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' \"'+atomid1+'\"\n')
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if atomid2 not in atomids2types:
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raise ttree_lex.InputError('Error: atom \"'+atomid2+'\" not defined in \"Data Atoms\".\n'
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' This usually happens when the user mistypes one of the names of the\n'
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' $atoms in either a \"Data Atoms\" or \"Data Bond List\" section.\n'
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' To find out where the mistake occured, search the \n'
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' \"ttree_assignments.txt\" file for:\n'
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' \"'+atomid2+'\"\n')
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atomtype1 = atomids2types[atomid1]
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atomtype2 = atomids2types[atomid2]
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# use string comparisons to check if atom types match the pattern
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if (ttree_lex.MatchesAll((atomtype1, atomtype2), typepattern) or
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ttree_lex.MatchesAll((atomtype2, atomtype1), typepattern)):
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@ -216,6 +216,7 @@ def LookupBondTypes(bond_types,
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for ie in range(0, len(bond_ids)):
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if not bond_types[ie]:
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(atomid1, atomid2) = bond_pairs[ie]
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atomtype1 = atomids2types[atomid1]
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atomtype2 = atomids2types[atomid2]
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raise ttree_lex.InputError('Error: No bond types defined for the bond between\n'
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@ -228,8 +229,8 @@ def LookupBondTypes(bond_types,
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if __name__ == "__main__":
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g_program_name = __file__.split('/')[-1] # = 'nbody_by_type.py'
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g_date_str = '2013-8-06'
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g_version_str = '0.1'
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g_date_str = '2015-11-09'
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g_version_str = '0.11'
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####### Main Code Below: #######
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sys.stderr.write(g_program_name+' v'+g_version_str+' '+g_date_str+' ')
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@ -217,8 +217,8 @@ def BelongsToSel(i, sel):
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try:
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g_program_name = __file__.split('/')[-1] # = 'ltemplify.py'
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g_version_str = '0.49'
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g_date_str = '2015-8-11'
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g_version_str = '0.51'
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g_date_str = '2015-10-27'
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sys.stderr.write(g_program_name+' v'+g_version_str+' '+g_date_str+'\n')
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non_empty_output = False
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@ -674,9 +674,12 @@ try:
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(boundary_ylo==None) or (boundary_yhi==None) or
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(boundary_zlo==None) or (boundary_zhi==None)):
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raise InputError('Error: The DATA file lacks a boundary-box header. You must specify:\n'
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raise InputError('Error: Either DATA file lacks a boundary-box header, or it is in the wrong\n'
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' place. At the beginning of the file, you need to specify the box size:\n'
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' xlo xhi ylo yhi zlo zhi (and xy xz yz if triclinic)\n'
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' These numbers should appear before the \"Atoms\" section.\n'
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' These numbers should appear BEFORE the other sections in the data file\n'
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' (such as the \"Atoms\", \"Masses\", \"Bonds\", \"Pair Coeffs\" sections)\n'
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'\n'
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' Use this format (example):\n'
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' -100.0 100.0 xhi xlo\n'
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' 0.0 200.0 yhi ylo\n'
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@ -788,8 +791,12 @@ try:
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tokens[i_molid] = '$mol:id'+tokens[i_molid]
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l_data_atoms.append((' '*indent)+(' '.join(tokens)+'\n'))
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needed_atomids.add(atomid)
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needed_atomtypes.add(atomtype)
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needed_molids.add(molid)
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# Not all atom_styles have molids.
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# Check for this before adding.
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if molid != None:
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needed_molids.add(molid)
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for atomtype in needed_atomtypes:
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assert(type(atomtype) is int)
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@ -808,7 +815,6 @@ try:
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if ((max_needed_atomid == None) or
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(max_needed_atomid < atomid)):
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max_needed_atomid = atomid
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for molid in needed_molids:
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assert(type(molid) is int)
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if ((min_needed_molid == None) or
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@ -731,7 +731,6 @@ if __name__ == "__main__":
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WriteFiles(files_content)
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sys.stderr.write(' done\n')
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# Step 11: Now write the variable bindings/assignments table.
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# Now write the variable bindings/assignments table.
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sys.stderr.write('writing \"ttree_assignments.txt\" file...')
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open('ttree_assignments.txt', 'w').close() # <-- erase previous version.
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@ -9,8 +9,8 @@
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# All rights reserved.
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G_PROGRAM_NAME="moltemplate.sh"
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G_VERSION="1.33"
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G_DATE="2015-9-22"
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G_VERSION="1.34"
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G_DATE="2015-11-18"
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echo "${G_PROGRAM_NAME} v${G_VERSION} ${G_DATE}" >&2
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echo "" >&2
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@ -27,7 +27,7 @@ else
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echo "Error: $G_PROGRAM_NAME requires python or python3" >&2
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exit 1
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fi
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# First, determine the directory in which this shell script is located.
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# (The python script files should also be located here as well.)
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@ -218,7 +218,7 @@ $data_ellipsoids
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$data_lines
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$data_triangles
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$data_boundary
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$data_bonds_by_type
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$data_bonds_by_type*
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${data_angles_by_type}*
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${data_dihedrals_by_type}*
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${data_impropers_by_type}*
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@ -599,6 +599,16 @@ done
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if [ -z "$ATOM_STYLE" ]; then
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#echo '########################################################\n' >&2
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#echo '## WARNING: atom_style unspecified ##\n' >&2
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#echo '## Assuming atom_style = \"full\" ##\n' >&2
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#echo '########################################################\n' >&2
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ATOM_STYLE="full"
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fi
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OUT_FILE_INPUT_SCRIPT="${OUT_FILE_BASE}.in"
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OUT_FILE_INIT="${OUT_FILE_BASE}.in.init"
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OUT_FILE_SETTINGS="${OUT_FILE_BASE}.in.settings"
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@ -736,13 +746,12 @@ if [ -s "${data_bond_list}.template" ]; then
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echo "Looking up bond types according to atom type" >&2
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#-- Generate a file containing bondid bondtype atomid1 atomid2 --
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if ! $PYTHON_COMMAND "${SCRIPT_DIR}/bonds_by_type.py" \
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-atom-style "$ATOM_STYLE" \
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-atoms "${data_atoms}.template" \
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-bond-list "${data_bond_list}.template" \
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-bondsbytype "${data_bonds_by_type}.template" \
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-prefix '$/bond:bytype' > gen_bonds.template.tmp; then
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exit 4
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#WARNING: DO NOT REPLACE THIS WITH
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#if ! $NBODY_COMMAND ...<-this sometimes causes a shell quotes-related error
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fi
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# ---- cleanup: ----
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@ -836,6 +845,7 @@ for FILE in "$data_angles_by_type"*.template; do
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-subgraph "${SUBGRAPH_SCRIPT}" \
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-section "Angles" \
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-sectionbytype "Angles By Type" \
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-atom-style "$ATOM_STYLE" \
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-atoms "${data_atoms}.template" \
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-bonds "${data_bonds}.template" \
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-nbodybytype "${FILE}" \
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@ -931,6 +941,7 @@ for FILE in "$data_dihedrals_by_type"*.template; do
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-subgraph "${SUBGRAPH_SCRIPT}" \
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-section "Dihedrals" \
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-sectionbytype "Dihedrals By Type" \
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-atom-style "$ATOM_STYLE" \
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-atoms "${data_atoms}.template" \
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-bonds "${data_bonds}.template" \
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-nbodybytype "${FILE}" \
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@ -1025,6 +1036,7 @@ for FILE in "$data_impropers_by_type"*.template; do
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-subgraph "${SUBGRAPH_SCRIPT}" \
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-section "Impropers" \
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-sectionbytype "Impropers By Type" \
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-atom-style "$ATOM_STYLE" \
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-atoms "${data_atoms}.template" \
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-bonds "${data_bonds}.template" \
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-nbodybytype "${FILE}" \
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@ -94,8 +94,8 @@ g_filename = __file__.split('/')[-1]
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g_module_name = g_filename
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if g_filename.rfind('.py') != -1:
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g_module_name = g_filename[:g_filename.rfind('.py')]
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g_date_str = '2015-8-17'
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g_version_str = '0.80'
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g_date_str = '2015-10-14'
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g_version_str = '0.81'
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@ -1676,7 +1676,15 @@ def LookupNode(obj_name, starting_node, dbg_loc):
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class SimpleCounter(object):
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__slots__=["n","nincr"]
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def __init__(self, n0 = 1, nincr = 1):
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# static data attributes:
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default_n0 = 1
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default_nincr = 1
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def __init__(self, n0 = None, nincr = None):
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if n0 == None:
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n0 = SimpleCounter.default_n0
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if nincr == None:
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nincr = SimpleCounter.default_nincr
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self.n = n0 - nincr
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self.nincr = nincr
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@ -1729,7 +1737,7 @@ class Category(object):
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self.bindings = bindings
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if counter is None:
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self.counter = SimpleCounter(1,1)
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self.counter = SimpleCounter()
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else:
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self.counter = counter
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