Commit f93cd8f7 authored by sjplimp's avatar sjplimp
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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@643 f3b2605a-c512-4ea7-a41b-209d697bcdaa
parent cea02082

tools/pymol_asphere/doc/asphere_vis.1

+8 −8
Original line number Diff line number Diff line 
.if !'\*(.T'ps' .if !'\*(.T'html' .tm warning: eqn should have been given a `-T\*(.T' option

.if '\*(.T'html' .if !'ps'ps' .tm warning: eqn should have been given a `-Tps' option

.if '\*(.T'html' .if !'ps'ps' .tm warning: (it is advisable to invoke groff via: groff -Thtml -e)

.lf 1 /usr/share/groff/1.18.1.1/tmac/eqnrc

.lf 1 /usr/share/groff/1.18.1/tmac/eqnrc

.\" Startup file for eqn.

.EQ

.nr 0C \n(.C
@@ -11,9 +11,9 @@ 
.lf 63

.EN

.lf 1 asphere_vis.manpage

.TH asphere_vis 1 "June 11, 2007" "asphere_vis (Graphics Utilities) 0.1" "Graphics Utilities"

.TH asphere_vis 1 "June 22, 2007" "asphere_vis (Graphics Utilities) 0.1" "Graphics Utilities"

.SH NAME

\fBasphere_vis\fR - Tools for LAMMPS ellipsoid trajectory visualization in PyMol.

\fBasphere_vis\fR - Tools for ellipsoid visualization in PyMol of a LAMMPS trajectory.

.PD 2

.SH VERSION

.PD 1
@@ -22,12 +22,12 @@ Version 0.1 
.SH SYNOPSIS

.PD 1

.TP

\fBasphere_vis\fR input_data_file input_dump_file output_py_file [\fB-b\fR] [\fB-c\fR \fIcolor_file\fR] [\fB-d\fR] [\fB-f\fR \fImax_frame\fR] [\fB-h\fR] [\fB-i\fR \fIstart_frame\fR \fIskip\fR \fIend_frame\fR] [\fB-n\fR \fInotice_level\fR] [\fB-r\fR \fIellip_res\fR] [\fB-s\fR]

\fBasphere_vis\fR input_file dump_file output_py_file [\fB-b\fR] [\fB-c\fR \fIcolor_file\fR] [\fB-d\fR] [\fB-f\fR \fImax_frame\fR] [\fB-h\fR] [\fB-i\fR \fIstart_frame\fR \fIskip\fR \fIend_frame\fR] [\fB-n\fR \fInotice_level\fR] [\fB-r\fR \fIellip_res\fR] [\fB-s\fR]

.br

.PD 2

.SH DESCRIPTION

.PD 1

Tool for LAMMPS trajectory visualization in PyMol. The input is a LAMMPS 'data' file or a 'in' file with ellipsoid semi-axes specified using the ellipsoid command. The trajectory is input from a 'dump' file that must be generated using a custom style with the following arguments in order:

Tool for ellipsoid visualization in PyMol of a LAMMPS trajectory. The \fIinput_file\fR is a LAMMPS data file with a 'Shapes' section or a LAMMPS input script file with ellipsoid diameters specified using the 'shape' command.  The trajectory is input from \fIdump_file\fR that must be generated using a LAMMPS dump_style custom command with the following arguments in order:

.PD 0

.PP

.PD 1
@@ -53,10 +53,10 @@ When used with \fB-s\fR, the option will number the filenames based on the frame 
.TP

.PP

.PD 1

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.

Color the atom_types and set transparency based on the color file. The color 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.

.TP

\fB-d\fR

Use a LAMMPS input file rather than a data file for extracting atom type information. The input filename is specified as \fIinput_data_file\fR.

Use a LAMMPS input script rather than a data file for extracting atom shape information. The input script is specified as \fIinput_file\fR.

.TP

\fB-f\fR \fImax_frame\fR

.PD 0
@@ -107,7 +107,7 @@ Set the degree of program output. Use: 
.TP

.PP

.PD 1

Resolution of ellipsoids in trajectory. The number of triangles per ellipsoid is equal to 2*(\fIellip_res\fR^2). Default is 10.

Resolution of ellipsoids in PyMol. The number of triangles per ellipsoid is equal to 2*(\fIellip_res\fR^2). Default is 10.

.TP

\fB-s\fR

Output the results into separate .py files. The filename and extension for the output files is taken from \fIoutput_py_file\fR.

tools/pymol_asphere/doc/asphere_vis.manpage

+7 −7
Original line number Diff line number Diff line 
.TH asphere_vis 1 "June 11, 2007" "asphere_vis (Graphics Utilities) 0.1" "Graphics Utilities"

.TH asphere_vis 1 "June 22, 2007" "asphere_vis (Graphics Utilities) 0.1" "Graphics Utilities"

.SH NAME

\fBasphere_vis\fR - Tools for LAMMPS ellipsoid trajectory visualization in PyMol.

\fBasphere_vis\fR - Tools for ellipsoid visualization in PyMol of a LAMMPS trajectory.

.PD 2

.SH VERSION

.PD 1
@@ -9,12 +9,12 @@ Version 0.1 
.SH SYNOPSIS

.PD 1

.TP

\fBasphere_vis\fR input_data_file input_dump_file output_py_file [\fB-b\fR] [\fB-c\fR \fIcolor_file\fR] [\fB-d\fR] [\fB-f\fR \fImax_frame\fR] [\fB-h\fR] [\fB-i\fR \fIstart_frame\fR \fIskip\fR \fIend_frame\fR] [\fB-n\fR \fInotice_level\fR] [\fB-r\fR \fIellip_res\fR] [\fB-s\fR]

\fBasphere_vis\fR input_file dump_file output_py_file [\fB-b\fR] [\fB-c\fR \fIcolor_file\fR] [\fB-d\fR] [\fB-f\fR \fImax_frame\fR] [\fB-h\fR] [\fB-i\fR \fIstart_frame\fR \fIskip\fR \fIend_frame\fR] [\fB-n\fR \fInotice_level\fR] [\fB-r\fR \fIellip_res\fR] [\fB-s\fR]

.br

.PD 2

.SH DESCRIPTION

.PD 1

Tool for LAMMPS trajectory visualization in PyMol. The input is a LAMMPS 'data' file or a 'in' file with ellipsoid semi-axes specified using the ellipsoid command. The trajectory is input from a 'dump' file that must be generated using a custom style with the following arguments in order:

Tool for ellipsoid visualization in PyMol of a LAMMPS trajectory. The \fIinput_file\fR is a LAMMPS data file with a 'Shapes' section or a LAMMPS input script file with ellipsoid diameters specified using the 'shape' command.  The trajectory is input from \fIdump_file\fR that must be generated using a LAMMPS dump_style custom command with the following arguments in order:

.PD 0

.PP

.PD 1
@@ -40,10 +40,10 @@ When used with \fB-s\fR, the option will number the filenames based on the frame 
.TP

.PP

.PD 1

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.

Color the atom_types and set transparency based on the color file. The color 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.

.TP

\fB-d\fR

Use a LAMMPS input file rather than a data file for extracting atom type information. The input filename is specified as \fIinput_data_file\fR.

Use a LAMMPS input script rather than a data file for extracting atom shape information. The input script is specified as \fIinput_file\fR.

.TP

\fB-f\fR \fImax_frame\fR

.PD 0
@@ -94,7 +94,7 @@ Set the degree of program output. Use: 
.TP

.PP

.PD 1

Resolution of ellipsoids in trajectory. The number of triangles per ellipsoid is equal to 2*(\fIellip_res\fR^2). Default is 10.

Resolution of ellipsoids in PyMol. The number of triangles per ellipsoid is equal to 2*(\fIellip_res\fR^2). Default is 10.

.TP

\fB-s\fR

Output the results into separate .py files. The filename and extension for the output files is taken from \fIoutput_py_file\fR.

tools/pymol_asphere/doc/asphere_vis.pdf

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tools/pymol_asphere/src/asphere_vis.cpp

+10 −10
Original line number Diff line number Diff line
@@ -339,20 +339,20 @@ void Describe(CommandLine &cl,ostream &out) { 
void HandleArgs(CommandLine &cl, int argc, char *argv[], Error *error) {

  // Arguments

  cl.addmanditory(' ',3);

  cl.addargname(' ',"input_data_file");

 cl.addargname(' ',"input_dump_file");

  cl.addargname(' ',"input_file");

 cl.addargname(' ',"dump_file");

 cl.addargname(' ',"output_py_file");

  cl.add('d',0);

  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.");

  cl.adddescription('d',"Use a LAMMPS input script rather than a data file for extracting atom shape information. The input script is specified as input_file.");

  cl.add('f',1);

  cl.addargname('f',"max_frame");

  cl.adddescription('f',"Do not write more than max_frame frames to the output file.");

  cl.add('r',1);

  cl.addargname('r',"ellip_res");

  cl.adddescription('r',"Resolution of ellipsoids in trajectory. The number of triangles per ellipsoid is equal to 2*(ellip_res^2). Default is 10.");

  cl.adddescription('r',"Resolution of ellipsoids in PyMol. The number of triangles per ellipsoid is equal to 2*(ellip_res^2). Default is 10.");

  cl.add('c',1);

  cl.addargname('c',"color_file");

  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.");

  cl.adddescription('c',"Color the atom_types and set transparency based on the color file. The color 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.");

  cl.add('s',0);

  cl.adddescription('s',"Output the results into separate .py files. The filename and extension for the output files is taken from output_py_file.");

  cl.add('i',3);
@@ -371,17 +371,17 @@ void HandleArgs(CommandLine &cl, int argc, char *argv[], Error *error) { 
  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");



  // Short Description

  cl.addtoman_chapter("NAME","Tools for LAMMPS ellipsoid trajectory visualization in PyMol.");

  cl.addtoman_chapter("NAME","Tools for ellipsoid visualization in PyMol of a LAMMPS trajectory.");



  // Version

  cl.addtoman_chapter("VERSION","Version 0.1");



  // Full Description

  const string desc[5]={

  "Tool for LAMMPS trajectory visualization in PyMol. The input is a LAMMPS ",

    "'data' file or a 'in' file with ellipsoid semi-axes specified using the ",

    "ellipsoid command. The trajectory is input from a 'dump' file that must ",

    "be generated using a custom style with the following arguments in order:\n",

  "Tool for ellipsoid visualization in PyMol of a LAMMPS trajectory. The input_file is a LAMMPS ",

    "data file with a 'Shapes' section or a LAMMPS input script file with ellipsoid diameters specified using the ",

    "'shape' command.  The trajectory is input from dump_file that must ",

    "be generated using a LAMMPS dump_style custom command with the following arguments in order:\n",

    ".TP\\fItag type x y z quatw quati quatj quatk\\fR\n"

 };

 cl.addtoman_chapter("DESCRIPTION",5,desc);

tools/restart2data.cpp

+28 −7
Original line number Diff line number Diff line
@@ -1886,6 +1886,12 @@ void angle(FILE *fp, Data &data) 
    fread(&data.angle_harmonic_k[1],sizeof(double),data.nangletypes,fp);

    fread(&data.angle_harmonic_theta0[1],sizeof(double),data.nangletypes,fp);



  } else if (strcmp(data.angle_style,"hybrid") == 0) {



    int nstyles = read_int(fp);

    for (int i = 0; i < nstyles; i++)

      char *substyle = read_char(fp);



  } else {

    printf("ERROR: Unknown angle style %s\n",data.angle_style);

    exit(1);
@@ -2065,6 +2071,12 @@ void dihedral(FILE *fp, Data &data) 
    fread(&data.dihedral_opls_k3[1],sizeof(double),data.ndihedraltypes,fp);

    fread(&data.dihedral_opls_k4[1],sizeof(double),data.ndihedraltypes,fp);



  } else if (strcmp(data.dihedral_style,"hybrid") == 0) {



    int nstyles = read_int(fp);

    for (int i = 0; i < nstyles; i++)

      char *substyle = read_char(fp);



  } else {

    printf("ERROR: Unknown dihedral style %s\n",data.dihedral_style);

    exit(1);
@@ -2128,6 +2140,12 @@ void improper(FILE *fp, Data &data) 
    fread(&data.improper_harmonic_chi[1],sizeof(double),

	  data.nimpropertypes,fp);



  } else if (strcmp(data.improper_style,"hybrid") == 0) {



    int nstyles = read_int(fp);

    for (int i = 0; i < nstyles; i++)

      char *substyle = read_char(fp);



  } else {

    printf("ERROR: Unknown improper style %s\n",data.improper_style);

    exit(1);
@@ -2361,10 +2379,11 @@ void Data::write(FILE *fp) 
  if (angle_style) {

    double PI = 3.1415926;           // convert back to degrees



    if (strcmp(angle_style,"none") != 0)

    if ((strcmp(angle_style,"none") != 0) && 

	(strcmp(angle_style,"hybrid") != 0))

      fprintf(fp,"\nAngle Coeffs\n\n");

    

    if (strcmp(angle_style,"charmm") == 0) {

    else if (strcmp(angle_style,"charmm") == 0) {

      for (int i = 1; i <= nangletypes; i++)

	fprintf(fp,"%d %g %g %g %g\n",i,

		angle_charmm_k[i],angle_charmm_theta0[i]/PI*180.0,
@@ -2403,10 +2422,11 @@ void Data::write(FILE *fp) 
  if (dihedral_style) {

    double PI = 3.1415926;           // convert back to degrees



    if (strcmp(dihedral_style,"none") != 0)

    if ((strcmp(dihedral_style,"none") != 0) && 

	(strcmp(dihedral_style,"hybrid") != 0))

      fprintf(fp,"\nDihedral Coeffs\n\n");



    if (strcmp(dihedral_style,"charmm") == 0) {

    else if (strcmp(dihedral_style,"charmm") == 0) {

      for (int i = 1; i <= ndihedraltypes; i++)

	fprintf(fp,"%d %g %d %d %g\n",i,

		dihedral_charmm_k[i],dihedral_charmm_multiplicity[i],
@@ -2485,10 +2505,11 @@ void Data::write(FILE *fp) 
  if (improper_style) {

    double PI = 3.1415926;           // convert back to degrees



    if (strcmp(improper_style,"none") != 0)

    if ((strcmp(improper_style,"none") != 0) && 

	(strcmp(improper_style,"hybrid") != 0))

      fprintf(fp,"\nImproper Coeffs\n\n");



    if (strcmp(improper_style,"class2") == 0) {

    else if (strcmp(improper_style,"class2") == 0) {

      for (int i = 1; i <= nimpropertypes; i++)

	fprintf(fp,"%d %g %g\n",i,

		improper_class2_k0[i],improper_class2_chi0[i]/PI*180.0);

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