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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@1084 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2007-10-22 21:36:28 +00:00
parent ddda2eeaf8
commit 01db99fbe5
8 changed files with 277 additions and 253 deletions
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5
tools/pymol_asphere/README
View File

@ -8,10 +8,7 @@ make # may need to edit Makefile for your system
This will place the asphere_vis executable in the bin directory.
Documentation is in the doc directory. Note that the doc file says
the ellipsoid axes are specified by an "Ellipsoid" section in the data
file. In the current version of LAMPS, this is now a "Shapes"
section.
Documentation is in the doc directory.
See instructions on how to run an example ellipsoid viz in the
examples dir.

74
tools/pymol_asphere/doc/asphere_vis.1
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@ -1,7 +1,7 @@
.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/tmac/eqnrc
.lf 1 /usr/share/groff/1.18.1.1/tmac/eqnrc
.\" Startup file for eqn.
.EQ
.nr 0C \n(.C
@ -11,36 +11,79 @@
.lf 63
.EN
.lf 1 asphere_vis.manpage
.TH asphere_vis 1 "June 22, 2007" "asphere_vis (Graphics Utilities) 0.1" "Graphics Utilities"
.TH asphere_vis 1 "October 22, 2007" "asphere_vis (Graphics Utilities) 0.2" "Graphics Utilities"
.SH NAME
\fBasphere_vis\fR - Tools for ellipsoid visualization in PyMol of a LAMMPS trajectory.
.PD 2
.SH VERSION
.PD 1
Version 0.1
Version 0.2
.PD 2
.SH SYNOPSIS
.PD 1
.TP
\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]
\fBasphere_vis\fR flavor_file dump_file output_py_file [\fB-b\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-o\fR] [\fB-r\fR \fIellip_res\fR] [\fB-s\fR]
.br
.PD 2
.SH DESCRIPTION
.PD 1
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:
Tool for converting LAMMPS trajectories into compiled graphics objects for visualization in PyMol. The \fIflavor_file\fR is an input file that describes the color, transparency, and size/shape of each atom type. The \fIflavor_file\fR consists of two possible line formats. For spherical particles, the format is:
.PD 0
.PP
.PD 1
.PD 0
.TP
.PP
.PD 1
\fItag type x y z quatw quati quatj quatk\fR
\fIatom_type color alpha diameter\fR
.PD 0
.PP
.PD 1
.PD 0
.PP
.PD 1
where alpha is used to adjust the transparency of the particle. For ellipsoidal particles, the format is:
.PD 0
.PP
.PD 1
.PD 0
.PP
.PD 1
\fIatom_type color alpha diameter_x diameter_y diameter_z\fR
.PD 0
.PP
.PD 1
.PD 0
.PP
.PD 1
Ellipsoidal and spherical line formats can be mixed in the same \fIflavor_file\fR For any atom type not listed in the \fIflavor_file\fR a blue sphere of size 1 is assumed.
.PD 0
.PP
.PD 1
.PD 0
.PP
.PD 1
The \fIdump_file\fR is a LAMMPS trajectory. For atom types specified as spherical in the \fIflavor_file\fR, the \fIdump_file\fR must contain \fItag type x y z\fR as the first columns. For atom types specified as ellipsoidal in the \fIflavor_file\fR, the columns are \fItag type x y z quatw quati quatj quatk\fR.The latter can be gerenated, for example, with the LAMMPS dump_style custom command with the following arguments in order:
.PD 0
.PP
.PD 1
.PD 0
.PP
.PD 1
\fItag type x y z quatw quati quatj quatk\fR
.PD 0
.PP
.PD 1
.PD 0
.PP
.PD 1
The output file is a python file for input to Pymol. This can be viewed from the command line using \fIpymol output.py\fR or by using the \fIrun\fR command from within Pymol.
.PD 2
.SH PARAMETERS
.PD 1
@ -48,16 +91,6 @@ Tool for ellipsoid visualization in PyMol of a LAMMPS trajectory. The \fIinput_f
\fB-b\fR
When used with \fB-s\fR, the option will number the filenames based on the frame number. By default, they are numbered consequtively from zero.
.TP
\fB-c\fR \fIcolor_file\fR
.PD 0
.TP
.PP
.PD 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 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
.TP
@ -102,6 +135,9 @@ Set the degree of program output. Use:
.PD 1
\fB-n\fR 30 All output
.TP
\fB-o\fR
Do not output the outline for the simulation box.
.TP
\fB-r\fR \fIellip_res\fR
.PD 0
.TP
@ -199,10 +235,6 @@ Output the results into separate .py files. The filename and extension for the o
.PP
.PD 1
.PD 2
.SH KNOWN BUGS
.PD 1
Comments are not allowed at any point between a section header and the end of the contents for a section in either the data file or the input file.
.PD 2
.SH AUTHORS
.PD 1

72
tools/pymol_asphere/doc/asphere_vis.manpage
View File

@ -1,33 +1,76 @@
.TH asphere_vis 1 "June 22, 2007" "asphere_vis (Graphics Utilities) 0.1" "Graphics Utilities"
.TH asphere_vis 1 "October 22, 2007" "asphere_vis (Graphics Utilities) 0.2" "Graphics Utilities"
.SH NAME
\fBasphere_vis\fR - Tools for ellipsoid visualization in PyMol of a LAMMPS trajectory.
.PD 2
.SH VERSION
.PD 1
Version 0.1
Version 0.2
.PD 2
.SH SYNOPSIS
.PD 1
.TP
\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]
\fBasphere_vis\fR flavor_file dump_file output_py_file [\fB-b\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-o\fR] [\fB-r\fR \fIellip_res\fR] [\fB-s\fR]
.br
.PD 2
.SH DESCRIPTION
.PD 1
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:
Tool for converting LAMMPS trajectories into compiled graphics objects for visualization in PyMol. The \fIflavor_file\fR is an input file that describes the color, transparency, and size/shape of each atom type. The \fIflavor_file\fR consists of two possible line formats. For spherical particles, the format is:
.PD 0
.PP
.PD 1
.PD 0
.TP
.PP
.PD 1
\fItag type x y z quatw quati quatj quatk\fR
\fIatom_type color alpha diameter\fR
.PD 0
.PP
.PD 1
.PD 0
.PP
.PD 1
where alpha is used to adjust the transparency of the particle. For ellipsoidal particles, the format is:
.PD 0
.PP
.PD 1
.PD 0
.PP
.PD 1
\fIatom_type color alpha diameter_x diameter_y diameter_z\fR
.PD 0
.PP
.PD 1
.PD 0
.PP
.PD 1
Ellipsoidal and spherical line formats can be mixed in the same \fIflavor_file\fR For any atom type not listed in the \fIflavor_file\fR a blue sphere of size 1 is assumed.
.PD 0
.PP
.PD 1
.PD 0
.PP
.PD 1
The \fIdump_file\fR is a LAMMPS trajectory. For atom types specified as spherical in the \fIflavor_file\fR, the \fIdump_file\fR must contain \fItag type x y z\fR as the first columns. For atom types specified as ellipsoidal in the \fIflavor_file\fR, the columns are \fItag type x y z quatw quati quatj quatk\fR.The latter can be gerenated, for example, with the LAMMPS dump_style custom command with the following arguments in order:
.PD 0
.PP
.PD 1
.PD 0
.PP
.PD 1
\fItag type x y z quatw quati quatj quatk\fR
.PD 0
.PP
.PD 1
.PD 0
.PP
.PD 1
The output file is a python file for input to Pymol. This can be viewed from the command line using \fIpymol output.py\fR or by using the \fIrun\fR command from within Pymol.
.PD 2
.SH PARAMETERS
.PD 1
@ -35,16 +78,6 @@ Tool for ellipsoid visualization in PyMol of a LAMMPS trajectory. The \fIinput_f
\fB-b\fR
When used with \fB-s\fR, the option will number the filenames based on the frame number. By default, they are numbered consequtively from zero.
.TP
\fB-c\fR \fIcolor_file\fR
.PD 0
.TP
.PP
.PD 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 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
.TP
@ -89,6 +122,9 @@ Set the degree of program output. Use:
.PD 1
\fB-n\fR 30 All output
.TP
\fB-o\fR
Do not output the outline for the simulation box.
.TP
\fB-r\fR \fIellip_res\fR
.PD 0
.TP
@ -186,10 +222,6 @@ Output the results into separate .py files. The filename and extension for the o
.PP
.PD 1
.PD 2
.SH KNOWN BUGS
.PD 1
Comments are not allowed at any point between a section header and the end of the contents for a section in either the data file or the input file.
.PD 2
.SH AUTHORS
.PD 1

BIN
tools/pymol_asphere/doc/asphere_vis.pdf
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Binary file not shown.

8
tools/pymol_asphere/examples/README
View File

@ -4,13 +4,13 @@ from a LAMMPS run.
In examples/ellipse, you can run LAMMPS with in.ellipse
to generate dump.ellipse
Copy in.ellipse and dump.ellipse to this dir.
Copy dump.ellipse to this dir.
Run the tool to create a PyMol input file called ellipse.py by typing:
../bin/asphere_vis in.ellipse dump.ellipse ellipse.py -c colors.ellipse -d
../bin/asphere_vis colors.ellipse dump.ellipse ellipse.py -r 4 -o
Launch PyMol on this input and you should see a nice viz of
4 ellipsoids in a box of LJ particles:
Launch PyMol on this input and you should see a viz of
ellipsoids in a box of LJ particles:
pymol ellipse.py

4
tools/pymol_asphere/examples/colors.ellipse
View File

@ -1,3 +1,3 @@
marine 0.3
red 1.0
1 marine 0.7 1
2 red 1.0 3 1 1

364
tools/pymol_asphere/src/asphere_vis.cpp
View File

@ -2,7 +2,7 @@
asphere_vis.cpp
-------------------
Convert a Lammps ellipsoid trajectory to a Pymol CGO trajectory
Convert a Lammps trajectory to a Pymol CGO trajectory
__________________________________________________________________________
This file is part of the Graphics Utilities package for command-line
@ -51,123 +51,62 @@ int main(int argc, char *argv[]) {
end_frame=cl.argint('i',2);
}
// ----------------- Get the atom type info from a data file
unsigned atom_types=0;
// ----------------- Assign default atom type info
unsigned max_atom_types=1000;
vector<cPt> shapes;
ifstream in;
if (!cl['d']) {
a::fileopen(in,cl.argstring(' ',0),error);
while (!in.eof()) {
char iline[500];
in.getline(iline,500);
vector<string> tokens;
a::get_tokens(iline,tokens);
if (tokens.size()>2)
if (tokens[1]=="atom" && tokens[2]=="types") {
atom_types=atoi(tokens[0].c_str());
break;
}
if (!in)
break;
}
if (atom_types==0)
error.generate_error(0,"asphere_vis",
"Could not find number of atom types in data file.");
// ----------------- Get the atom type shapes
if (parse_to("Shapes",in))
for (unsigned i=0; i<atom_types; i++) {
double tempd;
cPt shape;
in >> tempd >> shape;
shape.x *= 0.5;
shape.y *= 0.5;
shape.z *= 0.5;
if (in.eof() || !in)
break;
shapes.push_back(shape);
char iline[500];
in.getline(iline,500);
}
if (shapes.size()!=atom_types) {
error.buffer() << "Error reading shapes from Pair Coeffs section of "
<< "data file. Read " << shapes.size() << " valid shapes, "
<< "but expected " << atom_types;
error.addbuf(0,"asphere_vis");
}
a::fileclose(in,error);
} else {
// ----------------- Get the atom type info from a input file
a::fileopen(in,cl.argstring(' ',0),error);
while (!in.eof()) {
string token;
in >> token;
if (token=="create_box") {
in >> atom_types;
shapes.assign(atom_types,cPt(0.5,0.5,0.5));
} else if (token=="shape") {
unsigned type;
cPt shape;
in >> type >> shape;
shape.x *= 0.5;
shape.y *= 0.5;
shape.z *= 0.5;
if (type>atom_types) {
error.buffer() << "Error reading shapes from LAMMPS input file. "
<< "I thought there were " << atom_types
<< " atom types. But found an shape command for "
<< "atom type: " << type;
error.addbuf(0,"asphere_vis");
}
shapes[type-1]=shape;
} else {
char iline[500];
in.getline(iline,500);
}
if (!in && !in.eof())
error.generate_error(0,"asphere_vis",
"Error reading from LAMMPS input file");
}
a::fileclose(in,error);
}
if (atom_types==0)
error.generate_error(0,"asphere_vis","Found 0 atom types!");
// ----------------- Get the colors and alpha values for atom types
vector<colorPt> color_list;
vector<double> alpha_list;
if (cl['c']) {
a::fileopen(in,cl.argstring('c',0),error);
for (unsigned i=0; i<atom_types; i++) {
double alpha;
string color;
in >> color >> alpha;
if (in.eof() || !in)
error.generate_error(0,"asphere_vis",
"Improperly formatted color file.");
color_list.push_back(colors[color]);
alpha_list.push_back(alpha);
vector<bool> spherical;
shapes.assign(max_atom_types,cPt(0.5,0.5,0.5));
color_list.assign(max_atom_types,colors["blue"]);
alpha_list.assign(max_atom_types,1.0);
spherical.assign(max_atom_types,true);
// ----------------- Get the atom type info from a flavor file
unsigned atom_type;
cPt shape;
string color;
double alpha,diameter_x,diameter_y,diameter_z;
unsigned num_types=0;
char iline[5000];
ifstream in;
a::fileopen(in,cl.argstring(' ',0),error);
while (!in.eof()) {
in.getline(iline,500);
if (!in || in.eof())
break;
istringstream line_in(iline);
line_in >> atom_type;
if (!line_in || line_in.eof())
break;
if (atom_type>max_atom_types)
error.generate_error(0,"asphere_vis",
"asphere_vis will not handle atom types greater than "+
a::itoa(max_atom_types));
line_in >> color >> alpha >> diameter_x;
num_types++;
if (!line_in)
error.generate_error(0,"asphere_vis",
"Improperly formatted flavor_file at line:\n "+
string(iline));
color_list[atom_type]=colors[color];
alpha_list[atom_type]=alpha;
line_in >> diameter_y;
if (!line_in) {
shapes[atom_type].x=diameter_x/2.0;
continue;
}
a::fileclose(in,error);
line_in >> diameter_z;
if (!line_in)
error.generate_error(0,"asphere_vis",
"Improperly formatted flavor_file at line:\n "+
string(iline));
shapes[atom_type]=cPt(diameter_x/2.0,diameter_y/2.0,diameter_z/2.0);
spherical[atom_type]=false;
}
a::fileopen(in,cl.argstring(' ',1),error);
ofstream out;
if (!cl['s']) {
a::fileopen(out,cl.argstring(' ',2),error);
}
// ----------------- Get the atom count
unsigned atom_count;
if (parse_to("ITEM: NUMBER OF ATOMS",in))
in >> atom_count;
else
error.generate_error(0,"asphere_vis",
"Could not find ITEM: NUMBER OF ATOMS in input file.");
if (!in)
error.generate_error(0,"asphere_vis",
"Error reading ITEM: NUMBER OF ATOMS in input file.");
error.note[9] << "Read in " << num_types << " atom types from flavor_file.\n";
a::fileclose(in,error);
// ----------------- Get the triangles per ellipsoid
unsigned ellip_res=10;
@ -178,16 +117,21 @@ int main(int argc, char *argv[]) {
ellip_res=10;
}
// ----------------- Get the bounding box
bool bound_found=false;
a::fileopen(in,cl.argstring(' ',1),error);
ofstream out;
if (!cl['s']) {
a::fileopen(out,cl.argstring(' ',2),error);
}
// ----------------- Get the bounding box
GLSurface glb;
bool bound_found=false;
if (!cl['o']) {
if (parse_to("ITEM: BOX BOUNDS",in)) {
bound_found=true;
cPt bound[2];
in >> bound[0].x >> bound[1].x;
in >> bound[0].y >> bound[1].y;
in >> bound[0].z >> bound[1].z;
GLSurface gls;
in >> bound[0].x >> bound[1].x;
in >> bound[0].y >> bound[1].y;
in >> bound[0].z >> bound[1].z;
Vertex v;
v.transparency=1;
v.valid_normal=false;
@ -195,31 +139,33 @@ int main(int argc, char *argv[]) {
for (unsigned i=0; i<2; i++)
for (unsigned j=0; j<2; j++)
for (unsigned k=0; k<2; k++) {
v.cpt=cPt(bound[i].x,bound[j].y,bound[k].z);
gls.addvertex(v);
v.cpt=cPt(bound[i].x,bound[j].y,bound[k].z);
glb.addvertex(v);
}
gls.addline(0,1);
gls.addline(0,2);
gls.addline(0,4);
gls.addline(1,3);
gls.addline(1,5);
gls.addline(2,3);
gls.addline(2,6);
gls.addline(3,7);
gls.addline(4,5);
gls.addline(4,6);
gls.addline(5,7);
gls.addline(6,7);
gls.writelines(out,"gridb");
glb.addline(0,1);
glb.addline(0,2);
glb.addline(0,4);
glb.addline(1,3);
glb.addline(1,5);
glb.addline(2,3);
glb.addline(2,6);
glb.addline(3,7);
glb.addline(4,5);
glb.addline(4,6);
glb.addline(5,7);
glb.addline(6,7);
if (!cl['s'])
glb.writelines(out,"gridb");
out << "cmd.set('cgo_dot_width',8)\n";
} else
error.addwarning(0,9,"asphere_vis",
"Could not find ITEM: BOX BOUNDS in input file. No box output.");
}
if (!in)
error.generate_error(0,"asphere_vis",
"Error reading ITEM: BOX BOUNDS.");
if (!in)
error.generate_error(0,"asphere_vis",
"Error reading ITEM: BOX BOUNDS.");
a::fileclose(in,error);
// ----------------- Generate the frames
unsigned frame=0;
@ -227,11 +173,7 @@ int main(int argc, char *argv[]) {
if (cl['f'])
max_frame=cl.argint('f',0);
colorPt color=colors["marine"];
double alpha=1.0;
Vertex v;
v.color=color;
v.transparency=1.0;
a::fileopen(in,cl.argstring(' ',1),error);
// ----------------- Get to the start frame
while (frame<start_frame)
@ -242,49 +184,64 @@ int main(int argc, char *argv[]) {
frame++;
unsigned wrote=0;
Vertex v;
while (true) {
// ----------------- Get the atom count
unsigned atom_count;
if (parse_to("ITEM: NUMBER OF ATOMS",in))
in >> atom_count;
else
break;
if (!in)
error.generate_error(0,"asphere_vis",
"Error reading ITEM: NUMBER OF ATOMS in input file.");
if (frame>end_frame)
break;
if (!parse_to("ITEM: ATOMS",in))
break;
GLSurface gls;
for (unsigned i=0; i<atom_count; i++) {
unsigned id;
unsigned atom_type;
in >> id >> atom_type;
unsigned id, atom_type;
cPt atom_center;
in >> atom_center;
Quaternion q;
in >> q;
if (!in) {
error.addwarning(0,9,"asphere_vis","Error reading frame: "+
a::itoa(frame));
break;
}
cPt radius(shapes[atom_type-1]);
if (radius.x == radius.y && radius.y == radius.z) {
v.cpt=atom_center;
if (cl['c']) {
v.color=color_list[atom_type-1];
v.transparency=alpha_list[atom_type-1];
}
gls.addvertex(v);
gls.add_sphere(gls.size_vertices()-1,radius.x);
} else {
if (cl['c']) {
color=color_list[atom_type-1];
alpha=alpha_list[atom_type-1];
}
gls.add_ellipsoid(atom_center,radius,q,
color,alpha,ellip_res);
Quaternion q;
for (unsigned i=0; i<atom_count; i++) {
in.getline(iline,5000);
istringstream line_in(iline);
line_in >> id >> atom_type;
if (atom_type>max_atom_types)
error.generate_error(0,"asphere_vis",
"asphere_vis will not handle atom types greater than "+
a::itoa(max_atom_types));
line_in >> atom_center;
if (spherical[atom_type]==false)
line_in >> q;
if (!line_in) {
error.addwarning(0,9,"asphere_vis","Error reading frame: "+
a::itoa(frame));
break;
}
}
if (spherical[atom_type]) {
v.cpt=atom_center;
v.color=color_list[atom_type];
v.transparency=alpha_list[atom_type];
gls.addvertex(v);
gls.add_sphere(gls.size_vertices()-1,shapes[atom_type].x);
} else {
gls.add_ellipsoid(atom_center,shapes[atom_type],q,color_list[atom_type],
alpha_list[atom_type],ellip_res);
}
}
if (!in)
break;
if (cl['s']) {
if (cl['b'])
fi.set_file_num(frame);
a::fileopen(out,fi.nextfilename(),error);
if (!cl['o']) {
glb.writelines(out,"gridb");
out << "cmd.set('cgo_dot_width',8)\n";
}
}
gls.writetris(out,"ellipse");
if (gls.size_spheres()!=0)
@ -321,13 +278,13 @@ int main(int argc, char *argv[]) {
void Describe(CommandLine &cl,ostream &out) {
string name=cl.program_name();
string progname=a::strcenter(name,70);
string gridversion=a::strcenter("Graphics Library Version 0.1",70);
string gridversion=a::strcenter("Graphics Library Version 0.2",70);
out << endl << progname << endl << gridversion << endl
<< "______________________________________________________________________\n"
<< a::strcenter("W. Michael Brown",70) << endl
<< a::strcenter("1/12/2007",70) << endl
<< "______________________________________________________________________\n"
<< "Tool for LAMMPS aspherical trajectory visualization in pymol.\n\n"
<< "Tool for LAMMPS trajectory visualization in Pymol.\n\n"
<< cl.format_synopsis("","","") << endl << endl
<< "Use '" << name << " -h > " << name
<< ".1' to generate a man page for this\n"
@ -339,20 +296,15 @@ void Describe(CommandLine &cl,ostream &out) {
void HandleArgs(CommandLine &cl, int argc, char *argv[], Error *error) {
// Arguments
cl.addmanditory(' ',3);
cl.addargname(' ',"input_file");
cl.addargname(' ',"dump_file");
cl.addargname(' ',"output_py_file");
cl.add('d',0);
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.addargname(' ',"flavor_file");
cl.addargname(' ',"dump_file");
cl.addargname(' ',"output_py_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 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 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);
@ -362,6 +314,8 @@ void HandleArgs(CommandLine &cl, int argc, char *argv[], Error *error) {
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.");
cl.add('b',0);
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.");
cl.add('o',0);
cl.adddescription('o',"Do not output the outline for the simulation box.");
// Stuff for every executable
cl.addhelp('h',0);
@ -374,32 +328,40 @@ void HandleArgs(CommandLine &cl, int argc, char *argv[], Error *error) {
cl.addtoman_chapter("NAME","Tools for ellipsoid visualization in PyMol of a LAMMPS trajectory.");
// Version
cl.addtoman_chapter("VERSION","Version 0.1");
cl.addtoman_chapter("VERSION","Version 0.2");
// Full Description
const string desc[5]={
"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);
const string desc[22]={
"Tool for converting LAMMPS trajectories into compiled graphics objects for ",
"visualization in PyMol. The flavor_file is an input file that describes ",
"the color, transparency, and size/shape of each atom type. The flavor_file ",
"consists of two possible line formats. For spherical particles, the format ",
"is:\n\n",
"\t\\fIatom_type color alpha diameter\\fR\n\n",
"where alpha is used to adjust the transparency of the particle. For ",
"ellipsoidal particles, the format is:\n\n"
"\t\\fIatom_type color alpha diameter_x diameter_y diameter_z\\fR\n\n",
"Ellipsoidal and spherical line formats can be mixed in the same flavor_file ",
"For any atom type not listed in the flavor_file a blue sphere of size 1 is ",
"assumed.\n\n",
"The dump_file is a LAMMPS trajectory. For atom types specified as spherical ",
"in the flavor_file, the dump_file must contain \\fItag type x y z\\fR as ",
"the first columns. For atom types specified as ellipsoidal in the ",
"flavor_file, the columns are \\fItag type x y z quatw quati quatj quatk\\fR.",
"The latter can be gerenated, for example, with the ",
"LAMMPS dump_style custom command with the following arguments in order:\n\n",
"\t\\fItag type x y z quatw quati quatj quatk\\fR\n\n",
"The output file is a python file for input to Pymol. This can be viewed ",
"from the command line using \\fIpymol output.py\\fR or by using the \\fIrun\\fR ",
"command from within Pymol."
};
cl.addtoman_chapter("DESCRIPTION",22,desc);
Colors colors;
cl.addtoman_chapter("AVAILABLE COLORS",colors.colorlist());
// bugs
const string bugs[3]={
"Comments are not allowed at any point between a section header and ",
"the end of the contents for a section in either the data file or ",
"the input file."
};
cl.addtoman_chapter("KNOWN BUGS",3,bugs);
// Authors
cl.addtoman_chapter("AUTHORS","W. Michael Brown");
cl.addtoman_chapter("AUTHORS","W. Michael Brown");
// Parse the commandline
if (!cl.parse(argc,argv,error)) {
@ -420,7 +382,7 @@ void HandleArgs(CommandLine &cl, int argc, char *argv[], Error *error) {
// Output the help
if (cl['h']) {
cl.write_man_page(cout,"0.1","Graphics Utilities");
cl.write_man_page(cout,"0.2","Graphics Utilities");
exit(0);
}
}

1
tools/pymol_asphere/src/glsurface.cpp
View File

@ -535,6 +535,7 @@ void GLSurface::add_super_ellipsoid(const cPt &cen, const cPt &rad,
Vertex ver;
ver.color=color;
ver.transparency=alpha;
ver.valid_normal=true;
double dU=(u2-u1)/u_segs;
double dV=(v2-v1)/v_segs;
double U=u1;