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Super fix #307

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Super fix #307

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b40bcd0
return the correct transformation matrix
xivh Jul 25, 2023
4cbd73d
fix check for multiple --scelnames, --confignames, etc. without --duper
xivh Jul 25, 2023
0e1921b
reformat
xivh Jul 25, 2023
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195 changes: 92 additions & 103 deletions src/casm/app/super.cc
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Original file line number Diff line number Diff line change
Expand Up @@ -54,70 +54,59 @@ void SuperOption::initialize() {
add_configlists_nodefault_suboption();
add_coordtype_suboption();

m_desc.add_options()("transf-mat",
po::value<std::vector<fs::path> >(&m_transf_mat_paths)
->multitoken()
->value_name(ArgHandler::path()),
"1 or more files containing a 3x3 transformation matrix "
"used to create a supercell.")

("get-transf-mat", "If it exists, find the transformation matrix.")

("structure",
po::value<fs::path>(&m_struct_path)->value_name(ArgHandler::path()),
"File with structure (POSCAR type) to use.")

("unitcell",
po::value<std::string>(&m_unit_scel_str)
->value_name(ArgHandler::supercell()),
"Name of supercell to use as unit cell. For ex. "
"'SCEL2_2_1_1_0_0_0'.")

("duper",
"Construct the superduperlattice, the minimum supercell of "
"all input supercells "
"and configurations.")

("fixed-orientation",
"When constructing the superduperlattice, do not "
"consider other symmetrically "
"equivalent orientations.")

("min-volume", po::value<Index>(&m_min_vol),
"Transforms the transformation matrix, T -> T', "
"where T' = T*M, such that "
"(T').determininant() >= V. This has the effect "
"that a supercell has a "
"particular volume.")

("fixed-shape",
"Used with --min-volume to enforce that T' = "
"T*m*I, where I is the identity "
"matrix, and m is a scalar. This has the effect "
"of preserving the shape "
"of the resulting supercell, but increasing the "
"volume.")

("verbose",
"When used with --duper, show how the input "
"lattices are transformed "
"to tile the superduperlattice.")

("add-canonical,a",
"Will add the generated super "
"configuration in it's "
"canonical form in the equivalent "
"niggli supercell.")

("vasp5",
"Print using VASP5 style (include "
"atom name line)")

("tol",
po::value<double>(&m_tolerance)
->default_value(CASM::TOL),
"Tolerance used for checking "
"symmetry");
m_desc.add_options()(
"transf-mat",
po::value<std::vector<fs::path> >(&m_transf_mat_paths)
->multitoken()
->value_name(ArgHandler::path()),
"One or more files containing a 3x3 transformation matrix used to create "
"a supercell.")(

"get-transf-mat",
"If it exists, find the transformation matrix.")(

"structure",
po::value<fs::path>(&m_struct_path)->value_name(ArgHandler::path()),
"File with structure (POSCAR type) to use.")(

"unitcell",
po::value<std::string>(&m_unit_scel_str)
->value_name(ArgHandler::supercell()),
"Name of supercell to use as unit cell. For ex. 'SCEL2_2_1_1_0_0_0'.")(

"duper",
"Construct the superduperlattice, the minimum supercell of all input "
"supercells and configurations.")(

"fixed-orientation",
"When constructing the superduperlattice, do not consider other "
"symmetrically equivalent orientations.")(

"min-volume", po::value<Index>(&m_min_vol),
"Transforms the transformation matrix, T -> T', where T' = T*M, "
"such that (T').determininant() >= V. This has the effect "
"that a supercell has a particular volume.")(

"fixed-shape",
"Used with --min-volume to enforce that T' = T*m*I, where I is the "
"identity matrix, and m is a scalar. This has the effect of preserving "
"the shape of the resulting supercell, but increasing the volume.")(

"verbose",
"When used with --duper, show how the input lattices are transformed to "
"tile the superduperlattice.")(

"add-canonical,a",
"Will add the generated super configuration in its canonical form in the "
"equivalent niggli supercell.")(

"vasp5",
"Print using VASP5 style (include atom name line).")(

"tol",
po::value<double>(&m_tolerance)
->default_value(CASM::TOL),
"Tolerance used for checking symmetry");

return;
}
Expand Down Expand Up @@ -150,31 +139,6 @@ int super_command(const CommandArgs &args) {
po::parse_command_line(args.argc(), args.argv(), super_opt.desc()),
vm); // can throw

if (!vm.count("help") && !vm.count("desc")) {
if (!vm.count("duper")) {
if (vm.count("transf-mat") + vm.count("get-transf-mat") != 1) {
err_log() << "Error in 'casm super'. Only one of --transf-mat or "
"--get-transf-mat may be chosen."
<< std::endl;
return ERR_INVALID_ARG;
}
if (configname.size() > 1 || scelname.size() > 1 ||
tmatfile.size() > 1) {
err_log() << "ERROR: more than one --confignames, --scelnames, or "
"--transf-mat argument "
"is only allowed for option --duper"
<< std::endl;
return ERR_INVALID_ARG;
}
if (config_path.size() > 0) {
err_log() << "ERROR: the --configs option is only allowed with "
"option --duper"
<< std::endl;
return ERR_INVALID_ARG;
}
}
}

/** --help option
*/
if (vm.count("help")) {
Expand All @@ -184,7 +148,7 @@ int super_command(const CommandArgs &args) {
return 0;
}

if (vm.count("desc")) {
else if (vm.count("desc")) {
log() << "\n";
log() << super_opt.desc() << std::endl;
log() << "DESCRIPTION" << std::endl;
Expand Down Expand Up @@ -246,18 +210,43 @@ int super_command(const CommandArgs &args) {
return 0;
}

po::notify(vm); // throws on error, so do after help in case
// there are any problems

scelname = super_opt.supercell_strs();
configname = super_opt.config_strs();
unitscelname = super_opt.unit_scel_str();
structfile = super_opt.struct_path();
tmatfile = super_opt.transf_mat_paths();
config_path = super_opt.selection_paths();
min_vol = super_opt.min_vol();
tol = super_opt.tolerance();
coordtype = super_opt.coordtype_enum();
else {
po::notify(vm); // throws on error, so do after help in case
// there are any problems

scelname = super_opt.supercell_strs();
configname = super_opt.config_strs();
unitscelname = super_opt.unit_scel_str();
structfile = super_opt.struct_path();
tmatfile = super_opt.transf_mat_paths();
config_path = super_opt.selection_paths();
min_vol = super_opt.min_vol();
tol = super_opt.tolerance();
coordtype = super_opt.coordtype_enum();
if (!vm.count("duper")) {
if (vm.count("transf-mat") + vm.count("get-transf-mat") != 1) {
err_log() << "Error in 'casm super'. Only one of --transf-mat or "
"--get-transf-mat may be chosen."
<< std::endl;
return ERR_INVALID_ARG;
}
if (configname.size() > 1 || scelname.size() > 1 ||
tmatfile.size() > 1) {
err_log() << "ERROR: more than one --confignames, --scelnames, or "
"--transf-mat argument "
"is only allowed for option --duper"
<< std::endl;
return ERR_INVALID_ARG;
}
if (config_path.size() > 0) {
err_log() << "ERROR: the --configs option is only allowed with "
"option --duper"
<< std::endl;
return ERR_INVALID_ARG;
}
}
}

} catch (po::error &e) {
err_log() << "ERROR: " << e.what() << std::endl << std::endl;
err_log() << super_opt.desc() << std::endl;
Expand Down Expand Up @@ -699,7 +688,7 @@ int super_command(const CommandArgs &args) {
super_lat =
BasicStructure::from_poscar_stream(abs_structfile_stream).lattice();
} else if (vm.count("scelnames")) {
super_lat = primclex.db<Supercell>().find(unitscelname)->lattice();
super_lat = primclex.db<Supercell>().find(scelname[0])->lattice();
} else {
log() << "Error in 'casm super --get-transf-mat'. No --structure or "
"--scelnames given."
Expand Down