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| subroutine, public | prg_system_mod::prg_get_nameandext (fullfilename, filename, ext) |
| | Get the name and extension of a file. More...
|
| |
| subroutine, public | prg_system_mod::prg_parse_system (system, filename, extin) |
| | The parser for the chemical system. More...
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| |
| subroutine, public | prg_system_mod::prg_destroy_system (sy) |
| | Deallocates all the arrays within a system. More...
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| subroutine, public | prg_system_mod::prg_destroy_estr (estr) |
| | Deallocates all the arrays within the electronic structure. More...
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| |
| subroutine, public | prg_system_mod::prg_write_system (system, filename, extin) |
| | Write system in .xyz, .dat or pdb file. More...
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| |
| subroutine, public | prg_system_mod::prg_write_trajectory (system, iter, each, prg_deltat, filename, extension) |
| | Write trajectory in .xyz, .dat or pdb file. More...
|
| |
| subroutine, public | prg_system_mod::prg_write_trajectoryandproperty (system, iter, each, prg_deltat, scalarprop, filename, extension) |
| | Write trajectory and atomic properties. Only pdb file. More...
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| |
| subroutine, public | prg_system_mod::prg_make_random_system (system, nats, seed, lx, ly, lz) |
| | Make random Xx system. More...
|
| |
| subroutine, public | prg_system_mod::prg_parameters_to_vectors (abc_angles, lattice_vector) |
| | Transforms the lattice parameters into lattice vectors. More...
|
| |
| subroutine, public | prg_system_mod::prg_vectors_to_parameters (lattice_vector, abc_angles) |
| | Transforms the lattice vectors into lattice parameters. More...
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| subroutine, public | prg_system_mod::prg_get_origin (coords, origin) |
| | Get the origin of the coordinates. More...
|
| |
| subroutine, public | prg_system_mod::prg_get_distancematrix (coords, dmat) |
| | Get the distance matrix. More...
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| |
| subroutine, public | prg_system_mod::prg_translateandfoldtobox (coords, lattice_vectors, origin, verbose) |
| | Translate and fold to box. More...
|
| |
| subroutine, public | prg_system_mod::prg_centeratbox (coords, lattice_vectors, verbose) |
| | Translate geometric center to the center of the box. More...
|
| |
| subroutine, public | prg_system_mod::prg_wraparound (coords, lattice_vectors, index, verbose) |
| | Wrap around atom i using pbc. More...
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| |
| subroutine, public | prg_system_mod::prg_translatetogeomcandfoldtobox (coords, lattice_vectors, origin) |
| | Translate to geometric center. More...
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| subroutine, public | prg_system_mod::prg_replicate (coords, symbols, lattice_vectors, nx, ny, nz) |
| | Extend/replicate system along lattice vectors. More...
|
| |
| subroutine, public | prg_system_mod::prg_replicate_system (sy, syf, nx, ny, nz) |
| | Extend/replicate a system type along the lattice vectors. More...
|
| |
| subroutine, public | prg_system_mod::prg_cleanuprepeatedatoms (nats, coords, symbols, verbose) |
| | Cleanup repeated atoms we might have in the system. More...
|
| |
| subroutine, public | prg_system_mod::prg_get_recip_vects (lattice_vectors, recip_vectors, volr, volk) |
| | Get the volume of the cell and the reciprocal vectors: This soubroutine computes: More...
|
| |
| subroutine, public | prg_system_mod::prg_get_dihedral (coords, id1, id2, id3, id4, dihedral) |
| | Get the dihedral angle given four atomic positions. More...
|
| |
| subroutine, public | prg_system_mod::prg_get_covgraph (sy, nnStruct, nrnnstruct, bml_type, factor, gcov_bml, mdimin, verbose) |
| | Get the covalency graph in bml format. More...
|
| |
| subroutine | prg_system_mod::prg_get_covgraph_int (sy, nnStructMindist, nnStruct, nrnnstruct, bml_type, factor, gcov_bml, mdimin, verbose) |
| |
| subroutine, public | prg_system_mod::prg_get_covgraph_h (sy, nnStruct, nrnnstruct, rcut, graph_h, mdimin, verbose) |
| | Get the covanlency graph. More...
|
| |
| subroutine, public | prg_system_mod::prg_get_subsystem (sy, lsize, indices, sbsy, verbose) |
| | Get a subsystem out of the total system. More...
|
| |
| subroutine, public | prg_system_mod::prg_destroy_subsystems (sbsy, verbose) |
| | Destroy allocated subsystem. More...
|
| |
| subroutine, public | prg_system_mod::prg_molpartition (sy, npart, nnStructMindist, nnStruct, nrnnstruct, hetatm, gp, verbose) |
| | Partition by molecule. More...
|
| |
| subroutine, public | prg_system_mod::prg_get_partial_atomgraph (rho_bml, hindex, gch_bml, threshold, verbose) |
| | Get partial subgraph based on the Density matrix. More...
|
| |
| subroutine, public | prg_system_mod::prg_collect_graph_p (rho_bml, nc, nats, hindex, chindex, graph_p, threshold, mdimin, verbose) |
| | Collect the small graph to build the full graph. More...
|
| |
| subroutine, public | prg_system_mod::prg_merge_graph (graph_p, graph_h) |
| | Get partial subgraph based on the Density matrix. More...
|
| |
| subroutine, public | prg_system_mod::prg_merge_graph_adj (graph_p, graph_h, xadj, adjncy) |
| | Get partial subgraph based on the Density matrix. More...
|
| |
| subroutine, public | prg_system_mod::prg_adj2bml (xadj, adjncy, bml_type, g_bml) |
| | prg_adj2bml More...
|
| |
| subroutine, public | prg_system_mod::prg_graph2bml (graph, bml_type, g_bml) |
| | Graph2bml. More...
|
| |
| subroutine, public | prg_system_mod::prg_graph2vector (graph, vector, maxnz) |
| | Vectorize graph. More...
|
| |
| subroutine, public | prg_system_mod::prg_vector2graph (vector, graph, maxnz) |
| | Back to graph. More...
|
| |
| subroutine, public | prg_system_mod::prg_sortadj (xadj, adjncy) |
| | Sort adj NOTE: this might not be needed anymre since the bml_get_adj routine is sorting the values. More...
|
| |
1.9.1