git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@641 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
438
tools/pymol_asphere/src/asphere_vis.cpp
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438
tools/pymol_asphere/src/asphere_vis.cpp
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/***************************************************************************
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asphere_vis.cpp
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-------------------
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Convert a Lammps ellipsoid trajectory to a Pymol CGO trajectory
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__________________________________________________________________________
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This file is part of the Graphics Utilities package for command-line
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access to Graphics Library functions
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__________________________________________________________________________
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begin : Fri Jan 12 2007
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copyright : (C) 2007 by W. Michael Brown
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email : wmbrown@sandia.gov
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***************************************************************************/
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#include "commandline.h"
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#include "glsurface.h"
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#include <limits>
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// Describe the program parameters
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void Describe(CommandLine &cl,ostream &out);
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// Parse the command line parameters
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void HandleArgs(CommandLine &cl, int argc, char *argv[], Error *error);
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// Parse past an ITEM line in the lammps dump file
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bool parse_to(const char *token,ifstream &in);
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int main(int argc, char *argv[]) {
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CommandLine cl;
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Error error;
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Colors colors;
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FileIterator fi;
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// Parse the command line
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HandleArgs(cl,argc,argv,&error);
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// ----------------- Set up file names
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if (cl['s']) {
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fi.set_file_header(a::namewoext(cl.argstring(' ',2))+".");
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fi.set_file_extensions("."+a::extension(cl.argstring(' ',2)));
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fi.set_lead_zeros(4);
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}
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// ----------------- Get the frame interval
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unsigned start_frame=0;
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unsigned skip=0;
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unsigned end_frame=std::numeric_limits<unsigned>::max();
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if (cl['i']) {
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start_frame=cl.argint('i',0);
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skip=cl.argint('i',1);
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end_frame=cl.argint('i',2);
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}
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// ----------------- Get the atom type info from a data file
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unsigned atom_types=0;
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vector<cPt> shapes;
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ifstream in;
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if (!cl['d']) {
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a::fileopen(in,cl.argstring(' ',0),error);
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while (!in.eof()) {
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char iline[500];
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in.getline(iline,500);
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vector<string> tokens;
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a::get_tokens(iline,tokens);
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if (tokens.size()>2)
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if (tokens[1]=="atom" && tokens[2]=="types") {
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atom_types=atoi(tokens[0].c_str());
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break;
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}
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if (!in)
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break;
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}
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if (atom_types==0)
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error.generate_error(0,"asphere_vis",
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"Could not find number of atom types in data file.");
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// ----------------- Get the atom type shapes
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if (parse_to("Shapes",in))
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for (unsigned i=0; i<atom_types; i++) {
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double tempd;
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cPt shape;
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in >> tempd >> shape;
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shape.x *= 0.5;
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shape.y *= 0.5;
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shape.z *= 0.5;
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if (in.eof() || !in)
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break;
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shapes.push_back(shape);
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char iline[500];
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in.getline(iline,500);
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}
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if (shapes.size()!=atom_types) {
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error.buffer() << "Error reading shapes from Pair Coeffs section of "
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<< "data file. Read " << shapes.size() << " valid shapes, "
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<< "but expected " << atom_types;
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error.addbuf(0,"asphere_vis");
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}
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a::fileclose(in,error);
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} else {
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// ----------------- Get the atom type info from a input file
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a::fileopen(in,cl.argstring(' ',0),error);
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while (!in.eof()) {
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string token;
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in >> token;
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if (token=="create_box") {
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in >> atom_types;
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shapes.assign(atom_types,cPt(0.5,0.5,0.5));
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} else if (token=="shape") {
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unsigned type;
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cPt shape;
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in >> type >> shape;
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shape.x *= 0.5;
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shape.y *= 0.5;
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shape.z *= 0.5;
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if (type>atom_types) {
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error.buffer() << "Error reading shapes from LAMMPS input file. "
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<< "I thought there were " << atom_types
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<< " atom types. But found an shape command for "
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<< "atom type: " << type;
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error.addbuf(0,"asphere_vis");
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}
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shapes[type-1]=shape;
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} else {
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char iline[500];
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in.getline(iline,500);
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}
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if (!in && !in.eof())
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error.generate_error(0,"asphere_vis",
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"Error reading from LAMMPS input file");
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}
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a::fileclose(in,error);
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}
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if (atom_types==0)
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error.generate_error(0,"asphere_vis","Found 0 atom types!");
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// ----------------- Get the colors and alpha values for atom types
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vector<colorPt> color_list;
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vector<double> alpha_list;
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if (cl['c']) {
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a::fileopen(in,cl.argstring('c',0),error);
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for (unsigned i=0; i<atom_types; i++) {
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double alpha;
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string color;
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in >> color >> alpha;
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if (in.eof() || !in)
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error.generate_error(0,"asphere_vis",
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"Improperly formatted color file.");
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color_list.push_back(colors[color]);
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alpha_list.push_back(alpha);
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}
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a::fileclose(in,error);
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}
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a::fileopen(in,cl.argstring(' ',1),error);
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ofstream out;
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if (!cl['s']) {
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a::fileopen(out,cl.argstring(' ',2),error);
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}
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// ----------------- Get the atom count
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unsigned atom_count;
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if (parse_to("ITEM: NUMBER OF ATOMS",in))
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in >> atom_count;
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else
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error.generate_error(0,"asphere_vis",
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"Could not find ITEM: NUMBER OF ATOMS in input file.");
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if (!in)
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error.generate_error(0,"asphere_vis",
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"Error reading ITEM: NUMBER OF ATOMS in input file.");
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// ----------------- Get the triangles per ellipsoid
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unsigned ellip_res=10;
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if (cl['r'])
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ellip_res=cl.argint('r',0);
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if (ellip_res==0) {
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error.addwarning(0,9,"asphere_vis","Cannot use -r 0. Setting to 10.");
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ellip_res=10;
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}
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// ----------------- Get the bounding box
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bool bound_found=false;
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if (!cl['s']) {
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if (parse_to("ITEM: BOX BOUNDS",in)) {
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bound_found=true;
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cPt bound[2];
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in >> bound[0].x >> bound[1].x;
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in >> bound[0].y >> bound[1].y;
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in >> bound[0].z >> bound[1].z;
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GLSurface gls;
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Vertex v;
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v.transparency=1;
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v.valid_normal=false;
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v.color=colors["white"];
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for (unsigned i=0; i<2; i++)
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for (unsigned j=0; j<2; j++)
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for (unsigned k=0; k<2; k++) {
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v.cpt=cPt(bound[i].x,bound[j].y,bound[k].z);
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gls.addvertex(v);
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}
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gls.addline(0,1);
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gls.addline(0,2);
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gls.addline(0,4);
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gls.addline(1,3);
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gls.addline(1,5);
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gls.addline(2,3);
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gls.addline(2,6);
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gls.addline(3,7);
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gls.addline(4,5);
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gls.addline(4,6);
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gls.addline(5,7);
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gls.addline(6,7);
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gls.writelines(out,"gridb");
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out << "cmd.set('cgo_dot_width',8)\n";
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} else
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error.addwarning(0,9,"asphere_vis",
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"Could not find ITEM: BOX BOUNDS in input file. No box output.");
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}
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if (!in)
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error.generate_error(0,"asphere_vis",
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"Error reading ITEM: BOX BOUNDS.");
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// ----------------- Generate the frames
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unsigned frame=0;
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unsigned max_frame=std::numeric_limits<unsigned>::max();
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if (cl['f'])
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max_frame=cl.argint('f',0);
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colorPt color=colors["marine"];
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double alpha=1.0;
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Vertex v;
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v.color=color;
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v.transparency=1.0;
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// ----------------- Get to the start frame
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while (frame<start_frame)
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if (!parse_to("ITEM: ATOMS",in))
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error.generate_error(0,"asphere_vis",
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"Could not find first frame in interval in dump file.");
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else
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frame++;
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unsigned wrote=0;
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while (true) {
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if (frame>end_frame)
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break;
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if (!parse_to("ITEM: ATOMS",in))
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break;
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GLSurface gls;
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for (unsigned i=0; i<atom_count; i++) {
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unsigned id;
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unsigned atom_type;
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in >> id >> atom_type;
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cPt atom_center;
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in >> atom_center;
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Quaternion q;
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in >> q;
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if (!in) {
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error.addwarning(0,9,"asphere_vis","Error reading frame: "+
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a::itoa(frame));
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break;
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}
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cPt radius(shapes[atom_type-1]);
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if (radius.x == radius.y && radius.y == radius.z) {
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v.cpt=atom_center;
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if (cl['c']) {
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v.color=color_list[atom_type-1];
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v.transparency=alpha_list[atom_type-1];
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}
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gls.addvertex(v);
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gls.add_sphere(gls.size_vertices()-1,radius.x);
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} else {
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if (cl['c']) {
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color=color_list[atom_type-1];
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alpha=alpha_list[atom_type-1];
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}
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gls.add_ellipsoid(atom_center,radius,q,
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color,alpha,ellip_res);
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}
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}
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if (!in)
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break;
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if (cl['s']) {
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if (cl['b'])
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fi.set_file_num(frame);
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a::fileopen(out,fi.nextfilename(),error);
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}
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gls.writetris(out,"ellipse");
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if (gls.size_spheres()!=0)
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gls.writespheres(out,"spheres");
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if (cl['s'])
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a::fileclose(out,error);
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wrote++;
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frame++;
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if (frame==max_frame)
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break;
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for (unsigned i=0; i<skip; i++)
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if (!parse_to("ITEM: ATOMS",in))
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break;
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else
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frame++;
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}
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if (frame==0)
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error.addwarning(0,9,"asphere_vis",
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"Could not find any frams in input_file!");
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if (cl['i'] && frame<end_frame) {
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error.buffer() << "Only found " << frame << " frames in input file.";
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error.addbuf(0,9,"asphere_vis");
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}
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if (bound_found)
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out << "cmd.zoom(\"gridb\",animate=-1)\n";
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cout << "Wrote " << wrote << " frames to output file.\n";
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a::fileclose(out,error);
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return 0;
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}
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void Describe(CommandLine &cl,ostream &out) {
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string name=cl.program_name();
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string progname=a::strcenter(name,70);
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string gridversion=a::strcenter("Graphics Library Version 0.1",70);
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out << endl << progname << endl << gridversion << endl
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<< "______________________________________________________________________\n"
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<< a::strcenter("W. Michael Brown",70) << endl
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<< a::strcenter("1/12/2007",70) << endl
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<< "______________________________________________________________________\n"
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<< "Tool for LAMMPS aspherical trajectory visualization in pymol.\n\n"
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<< cl.format_synopsis("","","") << endl << endl
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<< "Use '" << name << " -h > " << name
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<< ".1' to generate a man page for this\n"
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<< "program and type 'man ./" << name << ".1' for help\n"
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<< "______________________________________________________________________\n";
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return;
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}
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void HandleArgs(CommandLine &cl, int argc, char *argv[], Error *error) {
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// Arguments
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cl.addmanditory(' ',3);
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cl.addargname(' ',"input_data_file");
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cl.addargname(' ',"input_dump_file");
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cl.addargname(' ',"output_py_file");
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cl.add('d',0);
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cl.adddescription('d',"Use a LAMMPS input file rather than a data file for extracting atom type information. The input filename is specified as input_data_file.");
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cl.add('f',1);
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cl.addargname('f',"max_frame");
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cl.adddescription('f',"Do not write more than max_frame frames to the output file.");
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cl.add('r',1);
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cl.addargname('r',"ellip_res");
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cl.adddescription('r',"Resolution of ellipsoids in trajectory. The number of triangles per ellipsoid is equal to 2*(ellip_res^2). Default is 10.");
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cl.add('c',1);
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cl.addargname('c',"color_file");
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cl.adddescription('c',"Color the atom_types and set transparency based on the input file. The input file contains a space delimited set sequence of the color for an atom followed by the alpha. The color should be the string name and the alpha should be between 0 and 1.");
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cl.add('s',0);
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cl.adddescription('s',"Output the results into separate .py files. The filename and extension for the output files is taken from output_py_file.");
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cl.add('i',3);
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cl.addargname('i',"start_frame");
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cl.addargname('i',"skip");
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cl.addargname('i',"end_frame");
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cl.adddescription('i',"Render the specified frame interval inclusive between start_frame and end_frame. skip gives the number of frames to skip between each rendered frame. A value of 0 outputs every frame between start_frame and end_frame. The first frame in the dump file is frame 0.");
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cl.add('b',0);
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cl.adddescription('b',"When used with -s, the option will number the filenames based on the frame number. By default, they are numbered consequtively from zero.");
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// Stuff for every executable
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cl.addhelp('h',0);
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cl.adddescription('h',"Print out the man page for help");
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cl.add('n',1);
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cl.addargname('n',"notice_level");
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cl.adddescription('n',"Set the degree of program output. Use: \n\n\t-n 0\tNo output\n\t-n 10\tNormal program output\n\t-n 20\tParameters useful for reproducing the results\n\t-n 30\tAll output");
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// Short Description
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cl.addtoman_chapter("NAME","Tools for LAMMPS ellipsoid trajectory visualization in PyMol.");
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// Version
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cl.addtoman_chapter("VERSION","Version 0.1");
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// Full Description
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const string desc[5]={
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"Tool for LAMMPS trajectory visualization in PyMol. The input is a LAMMPS ",
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"'data' file or a 'in' file with ellipsoid semi-axes specified using the ",
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"ellipsoid command. The trajectory is input from a 'dump' file that must ",
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"be generated using a custom style with the following arguments in order:\n",
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".TP\\fItag type x y z quatw quati quatj quatk\\fR\n"
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};
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cl.addtoman_chapter("DESCRIPTION",5,desc);
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Colors colors;
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cl.addtoman_chapter("AVAILABLE COLORS",colors.colorlist());
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// bugs
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const string bugs[3]={
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"Comments are not allowed at any point between a section header and ",
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"the end of the contents for a section in either the data file or ",
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"the input file."
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};
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cl.addtoman_chapter("KNOWN BUGS",3,bugs);
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// Authors
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cl.addtoman_chapter("AUTHORS","W. Michael Brown");
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// Parse the commandline
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if (!cl.parse(argc,argv,error)) {
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Describe(cl,cout);
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error->generate_error(0,a::filenameonly(argv[0]),"Bad Command Line\n");
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}
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// Set the notice level
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if (cl['n'])
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error->note.set_notice_level(cl.argint('n',0));
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// Generate a notice with the command line for records purposes
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string cm=cl.program_name();
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for (int j=1; j<argc; j++)
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cm+=' '+string(argv[j]);
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cm+="\n";
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error->note.notice(19,"CommandLine",cm);
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// Output the help
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if (cl['h']) {
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cl.write_man_page(cout,"0.1","Graphics Utilities");
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exit(0);
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}
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}
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// Parse past an ITEM line in the lammps dump file
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bool parse_to(const char * token,ifstream &in) {
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char iline[5000];
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while (true) {
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in.getline(iline,5000);
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if (in.eof() || !in)
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return false;
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if (strcmp(token,iline)==0)
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return true;
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}
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}
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Reference in New Issue
Block a user