forked from lijiext/lammps
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@7682 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
parent
b99a706744
commit
9b3b8d2f3a
|
|
@ -86,11 +86,12 @@ class Data {
|
|||
int newton_pair,newton_bond;
|
||||
int xperiodic,yperiodic,zperiodic;
|
||||
int boundary[3][2];
|
||||
|
||||
|
||||
char *atom_style;
|
||||
int style_angle,style_atomic,style_bond,style_charge,style_dipole;
|
||||
int style_ellipsoid,style_full;
|
||||
int style_hybrid,style_molecular,style_peri,style_sphere;
|
||||
int style_ellipsoid,style_full,style_line,style_meso;
|
||||
int style_molecular,style_peri,style_sphere;
|
||||
int style_tri,style_wavepacket,style_hybrid;
|
||||
|
||||
bigint natoms;
|
||||
bigint nellipsoids;
|
||||
|
|
@ -213,7 +214,7 @@ class Data {
|
|||
tagint *tag;
|
||||
int *type,*mask,*image;
|
||||
int *molecule;
|
||||
double *q,*mux,*muy,*muz,*radius,*density,*vfrac,*rmass;
|
||||
double *q,*mux,*muy,*muz,*mul,*radius,*density,*vfrac,*rmass;
|
||||
double *s0,*x0x,*x0y,*x0z;
|
||||
double *shapex,*shapey,*shapez;
|
||||
double *quatw,*quati,*quatj,*quatk,*angmomx,*angmomy,*angmomz;
|
||||
|
|
@ -228,7 +229,7 @@ class Data {
|
|||
|
||||
Data();
|
||||
void stats();
|
||||
void write(FILE *fp, FILE *fp2=NULL);
|
||||
void write(FILE *, FILE *, int, int);
|
||||
|
||||
void write_atom_angle(FILE *, int, int, int, int);
|
||||
void write_atom_atomic(FILE *, int, int, int, int);
|
||||
|
|
@ -237,9 +238,13 @@ class Data {
|
|||
void write_atom_dipole(FILE *, int, int, int, int);
|
||||
void write_atom_ellipsoid(FILE *, int, int, int, int);
|
||||
void write_atom_full(FILE *, int, int, int, int);
|
||||
void write_atom_line(FILE *, int, int, int, int);
|
||||
void write_atom_meso(FILE *, int, int, int, int);
|
||||
void write_atom_molecular(FILE *, int, int, int, int);
|
||||
void write_atom_peri(FILE *, int, int, int, int);
|
||||
void write_atom_sphere(FILE *, int, int, int, int);
|
||||
void write_atom_tri(FILE *, int, int, int, int);
|
||||
void write_atom_wavepacket(FILE *, int, int, int, int);
|
||||
|
||||
void write_atom_angle_extra(FILE *, int);
|
||||
void write_atom_atomic_extra(FILE *, int);
|
||||
|
|
@ -248,9 +253,13 @@ class Data {
|
|||
void write_atom_dipole_extra(FILE *, int);
|
||||
void write_atom_ellipsoid_extra(FILE *, int);
|
||||
void write_atom_full_extra(FILE *, int);
|
||||
void write_atom_line_extra(FILE *, int);
|
||||
void write_atom_meso_extra(FILE *, int);
|
||||
void write_atom_molecular_extra(FILE *, int);
|
||||
void write_atom_peri_extra(FILE *, int);
|
||||
void write_atom_sphere_extra(FILE *, int);
|
||||
void write_atom_tri_extra(FILE *, int);
|
||||
void write_atom_wavepacket_extra(FILE *, int);
|
||||
|
||||
void write_vel_angle(FILE *, int);
|
||||
void write_vel_atomic(FILE *, int);
|
||||
|
|
@ -259,9 +268,13 @@ class Data {
|
|||
void write_vel_dipole(FILE *, int);
|
||||
void write_vel_ellipsoid(FILE *, int);
|
||||
void write_vel_full(FILE *, int);
|
||||
void write_vel_line(FILE *, int);
|
||||
void write_vel_meso(FILE *, int);
|
||||
void write_vel_molecular(FILE *, int);
|
||||
void write_vel_peri(FILE *, int);
|
||||
void write_vel_sphere(FILE *, int);
|
||||
void write_vel_tri(FILE *, int);
|
||||
void write_vel_wavepacket(FILE *, int);
|
||||
|
||||
void write_vel_angle_extra(FILE *, int);
|
||||
void write_vel_atomic_extra(FILE *, int);
|
||||
|
|
@ -270,9 +283,13 @@ class Data {
|
|||
void write_vel_dipole_extra(FILE *, int);
|
||||
void write_vel_ellipsoid_extra(FILE *, int);
|
||||
void write_vel_full_extra(FILE *, int);
|
||||
void write_vel_line_extra(FILE *, int);
|
||||
void write_vel_meso_extra(FILE *, int);
|
||||
void write_vel_molecular_extra(FILE *, int);
|
||||
void write_vel_peri_extra(FILE *, int);
|
||||
void write_vel_sphere_extra(FILE *, int);
|
||||
void write_vel_tri_extra(FILE *, int);
|
||||
void write_vel_wavepacket_extra(FILE *, int);
|
||||
};
|
||||
|
||||
// ---------------------------------------------------------------------
|
||||
|
|
@ -299,9 +316,13 @@ void allocate_charge(Data &data);
|
|||
void allocate_dipole(Data &data);
|
||||
void allocate_ellipsoid(Data &data);
|
||||
void allocate_full(Data &data);
|
||||
void allocate_line(Data &data);
|
||||
void allocate_meso(Data &data);
|
||||
void allocate_molecular(Data &data);
|
||||
void allocate_peri(Data &data);
|
||||
void allocate_sphere(Data &data);
|
||||
void allocate_tri(Data &data);
|
||||
void allocate_wavepacket(Data &data);
|
||||
|
||||
int atom_angle(double *, Data &, int);
|
||||
int atom_atomic(double *, Data &, int);
|
||||
|
|
@ -310,9 +331,13 @@ int atom_charge(double *, Data &, int);
|
|||
int atom_dipole(double *, Data &, int);
|
||||
int atom_ellipsoid(double *, Data &, int);
|
||||
int atom_full(double *, Data &, int);
|
||||
int atom_line(double *, Data &, int);
|
||||
int atom_meso(double *, Data &, int);
|
||||
int atom_molecular(double *, Data &, int);
|
||||
int atom_peri(double *, Data &, int);
|
||||
int atom_sphere(double *, Data &, int);
|
||||
int atom_tri(double *, Data &, int);
|
||||
int atom_wavepacket(double *, Data &, int);
|
||||
|
||||
void strip_suffix(char *);
|
||||
|
||||
|
|
@ -321,6 +346,22 @@ double read_double(FILE *fp);
|
|||
char *read_char(FILE *fp);
|
||||
bigint read_bigint(FILE *fp);
|
||||
|
||||
static void helpmsg(int exitval)
|
||||
{
|
||||
printf("Syntax: restart2data (switch1 switch2 ...) "
|
||||
"restart-file data-file (input-file)\n");
|
||||
printf(" 'restart-file' and 'data-file' are mandatory\n");
|
||||
printf(" 'input-file' is optional\n");
|
||||
printf(" If specified, it will contain LAMMPS input script\n");
|
||||
printf(" commands for mass and force field info.\n");
|
||||
printf(" Only a few force field styles support this option.\n");
|
||||
printf(" Switches are optional. Supported switches:\n");
|
||||
printf(" -h print this message\n");
|
||||
printf(" -nc don't write out coefficients\n");
|
||||
printf(" -nv don't write out velocities\n");
|
||||
exit(exitval);
|
||||
}
|
||||
|
||||
// ---------------------------------------------------------------------
|
||||
// main program
|
||||
// ---------------------------------------------------------------------
|
||||
|
|
@ -329,24 +370,30 @@ int main (int narg, char **arg)
|
|||
{
|
||||
// process command-line args
|
||||
|
||||
int iarg = 1;
|
||||
if (narg < 2 || strcmp(arg[iarg],"-h") == 0) {
|
||||
printf("Syntax: restart2data (switch) ... "
|
||||
"restart-file data-file (input-file)\n");
|
||||
printf(" 'restart-file' and 'data-file' are mandatory\n");
|
||||
printf(" 'input-file' is optional\n");
|
||||
printf(" If specified, it will contain LAMMPS input script\n");
|
||||
printf(" commands for mass and force field info.\n");
|
||||
printf(" Only a few force field styles support this option.\n");
|
||||
printf(" 'switch' is optional\n");
|
||||
printf(" The only supported switch is '-h' to print this message\n");
|
||||
return 0;
|
||||
if (narg < 2) helpmsg(1);
|
||||
|
||||
int iarg,write_coeffs,write_vels;
|
||||
char *restartfile, *datafile, *inputfile;
|
||||
write_coeffs = write_vels = 1;
|
||||
restartfile = datafile = inputfile = NULL;
|
||||
|
||||
for (iarg = 1; iarg < narg; ++iarg) {
|
||||
if (strcmp(arg[iarg],"-h") == 0) {
|
||||
helpmsg(0);
|
||||
} else if (strcmp(arg[iarg],"-nc") == 0) {
|
||||
write_coeffs = 0;
|
||||
} else if (strcmp(arg[iarg],"-nv") == 0) {
|
||||
write_vels = 0;
|
||||
} else if (!restartfile) {
|
||||
restartfile = arg[iarg];
|
||||
} else if (!datafile) {
|
||||
datafile = arg[iarg];
|
||||
} else if (!inputfile) {
|
||||
inputfile = arg[iarg];
|
||||
}
|
||||
}
|
||||
|
||||
char *restartfile = arg[iarg];
|
||||
char *datafile = arg[iarg+1];
|
||||
char *inputfile = NULL;
|
||||
if (narg-iarg == 3) inputfile = arg[iarg+2];
|
||||
if (!restartfile || !datafile) helpmsg(2);
|
||||
|
||||
// if restart file contains '%', file = filename with % replaced by "base"
|
||||
// else file = single file
|
||||
|
|
@ -442,7 +489,7 @@ int main (int narg, char **arg)
|
|||
printf("ERROR: Cannot open data file %s\n",datafile);
|
||||
return 1;
|
||||
}
|
||||
data.write(fp);
|
||||
data.write(fp,NULL,write_coeffs,write_vels);
|
||||
fclose(fp);
|
||||
|
||||
// write out data file and input file
|
||||
|
|
@ -461,7 +508,7 @@ int main (int narg, char **arg)
|
|||
return 1;
|
||||
}
|
||||
|
||||
data.write(fp,fp2);
|
||||
data.write(fp,fp2,write_coeffs,write_vels);
|
||||
fclose(fp);
|
||||
fclose(fp2);
|
||||
}
|
||||
|
|
@ -475,7 +522,7 @@ int main (int narg, char **arg)
|
|||
|
||||
void header(FILE *fp, Data &data)
|
||||
{
|
||||
const char *version = "31 Jan 2012";
|
||||
const char *version = "6 Feb 2012";
|
||||
|
||||
data.triclinic = 0;
|
||||
|
||||
|
|
@ -522,9 +569,10 @@ void header(FILE *fp, Data &data)
|
|||
|
||||
else if (flag == ATOM_STYLE) {
|
||||
data.style_angle = data.style_atomic = data.style_bond =
|
||||
data.style_charge = data.style_dipole =
|
||||
data.style_ellipsoid = data.style_full = data.style_hybrid =
|
||||
data.style_molecular = data.style_peri = data.style_sphere = 0;
|
||||
data.style_charge = data.style_dipole = data.style_ellipsoid =
|
||||
data.style_full = data.style_line = data.style_meso =
|
||||
data.style_molecular = data.style_peri = data.style_sphere =
|
||||
data.style_tri = data.style_wavepacket = data.style_hybrid = 0;
|
||||
|
||||
data.atom_style = read_char(fp);
|
||||
strip_suffix(data.atom_style);
|
||||
|
|
@ -599,10 +647,14 @@ void set_style(char *name, Data &data, int flag)
|
|||
else if (strcmp(name,"dipole") == 0) data.style_dipole = flag;
|
||||
else if (strcmp(name,"ellipsoid") == 0) data.style_ellipsoid = flag;
|
||||
else if (strcmp(name,"full") == 0) data.style_full = flag;
|
||||
else if (strcmp(name,"hybrid") == 0) data.style_hybrid = flag;
|
||||
else if (strcmp(name,"line") == 0) data.style_line = flag;
|
||||
else if (strcmp(name,"meso") == 0) data.style_meso = flag;
|
||||
else if (strcmp(name,"molecular") == 0) data.style_molecular = flag;
|
||||
else if (strcmp(name,"peri") == 0) data.style_peri = flag;
|
||||
else if (strcmp(name,"sphere") == 0) data.style_sphere = flag;
|
||||
else if (strcmp(name,"tri") == 0) data.style_tri = flag;
|
||||
else if (strcmp(name,"wavepacket") == 0) data.style_wavepacket = flag;
|
||||
else if (strcmp(name,"hybrid") == 0) data.style_hybrid = flag;
|
||||
else {
|
||||
printf("ERROR: Unknown atom style %s\n",name);
|
||||
exit(1);
|
||||
|
|
@ -768,9 +820,13 @@ int atom(double *buf, Data &data)
|
|||
if (data.style_dipole) allocate_dipole(data);
|
||||
if (data.style_ellipsoid) allocate_ellipsoid(data);
|
||||
if (data.style_full) allocate_full(data);
|
||||
if (data.style_line) allocate_line(data);
|
||||
if (data.style_meso) allocate_meso(data);
|
||||
if (data.style_molecular) allocate_molecular(data);
|
||||
if (data.style_peri) allocate_peri(data);
|
||||
if (data.style_sphere) allocate_sphere(data);
|
||||
if (data.style_tri) allocate_tri(data);
|
||||
if (data.style_wavepacket) allocate_wavepacket(data);
|
||||
}
|
||||
|
||||
// read atom quantities from buf
|
||||
|
|
@ -790,9 +846,13 @@ int atom(double *buf, Data &data)
|
|||
if (k == data.style_dipole) m += atom_dipole(&buf[m],data,iatoms);
|
||||
if (k == data.style_ellipsoid) m += atom_ellipsoid(&buf[m],data,iatoms);
|
||||
if (k == data.style_full) m += atom_full(&buf[m],data,iatoms);
|
||||
if (k == data.style_line) m += atom_line(&buf[m],data,iatoms);
|
||||
if (k == data.style_meso) m += atom_meso(&buf[m],data,iatoms);
|
||||
if (k == data.style_molecular) m += atom_molecular(&buf[m],data,iatoms);
|
||||
if (k == data.style_peri) m += atom_peri(&buf[m],data,iatoms);
|
||||
if (k == data.style_sphere) m += atom_sphere(&buf[m],data,iatoms);
|
||||
if (k == data.style_tri) m += atom_tri(&buf[m],data,iatoms);
|
||||
if (k == data.style_wavepacket) m += atom_wavepacket(&buf[m],data,iatoms);
|
||||
}
|
||||
|
||||
data.iatoms++;
|
||||
|
|
@ -940,7 +1000,7 @@ int atom_dipole(double *buf, Data &data, int iatoms)
|
|||
data.mux[iatoms] = buf[m++];
|
||||
data.muy[iatoms] = buf[m++];
|
||||
data.muz[iatoms] = buf[m++];
|
||||
|
||||
data.mul[iatoms] = buf[m++];
|
||||
return m;
|
||||
}
|
||||
|
||||
|
|
@ -981,34 +1041,6 @@ int atom_ellipsoid(double *buf, Data &data, int iatoms)
|
|||
return m;
|
||||
}
|
||||
|
||||
int atom_sphere(double *buf, Data &data, int iatoms)
|
||||
{
|
||||
int m = 1;
|
||||
data.x[iatoms] = buf[m++];
|
||||
data.y[iatoms] = buf[m++];
|
||||
data.z[iatoms] = buf[m++];
|
||||
data.tag[iatoms] = static_cast<int> (buf[m++]);
|
||||
data.type[iatoms] = static_cast<int> (buf[m++]);
|
||||
data.mask[iatoms] = static_cast<int> (buf[m++]);
|
||||
data.image[iatoms] = static_cast<int> (buf[m++]);
|
||||
data.vx[iatoms] = buf[m++];
|
||||
data.vy[iatoms] = buf[m++];
|
||||
data.vz[iatoms] = buf[m++];
|
||||
|
||||
data.radius[iatoms] = buf[m++];
|
||||
data.rmass[iatoms] = buf[m++];
|
||||
if (data.radius[iatoms] == 0.0) data.density[iatoms] = data.rmass[iatoms];
|
||||
else
|
||||
data.density[iatoms] = data.rmass[iatoms] /
|
||||
(4.0*PI/3.0 *
|
||||
data.radius[iatoms]*data.radius[iatoms]*data.radius[iatoms]);
|
||||
data.omegax[iatoms] = buf[m++];
|
||||
data.omegay[iatoms] = buf[m++];
|
||||
data.omegaz[iatoms] = buf[m++];
|
||||
|
||||
return m;
|
||||
}
|
||||
|
||||
int atom_full(double *buf, Data &data, int iatoms)
|
||||
{
|
||||
int type,atom1,atom2,atom3,atom4;
|
||||
|
|
@ -1092,6 +1124,18 @@ int atom_full(double *buf, Data &data, int iatoms)
|
|||
return m;
|
||||
}
|
||||
|
||||
int atom_line(double *buf, Data &data, int iatoms)
|
||||
{
|
||||
fprintf(stderr,"support for atom style line is not fully implemented\n");
|
||||
exit(1);
|
||||
}
|
||||
|
||||
int atom_meso(double *buf, Data &data, int iatoms)
|
||||
{
|
||||
fprintf(stderr,"support for atom style meso is not fully implemented\n");
|
||||
exit(1);
|
||||
}
|
||||
|
||||
int atom_molecular(double *buf, Data &data, int iatoms)
|
||||
{
|
||||
int type,atom1,atom2,atom3,atom4;
|
||||
|
|
@ -1198,6 +1242,46 @@ int atom_peri(double *buf, Data &data, int iatoms)
|
|||
return m;
|
||||
}
|
||||
|
||||
int atom_sphere(double *buf, Data &data, int iatoms)
|
||||
{
|
||||
int m = 1;
|
||||
data.x[iatoms] = buf[m++];
|
||||
data.y[iatoms] = buf[m++];
|
||||
data.z[iatoms] = buf[m++];
|
||||
data.tag[iatoms] = static_cast<int> (buf[m++]);
|
||||
data.type[iatoms] = static_cast<int> (buf[m++]);
|
||||
data.mask[iatoms] = static_cast<int> (buf[m++]);
|
||||
data.image[iatoms] = static_cast<int> (buf[m++]);
|
||||
data.vx[iatoms] = buf[m++];
|
||||
data.vy[iatoms] = buf[m++];
|
||||
data.vz[iatoms] = buf[m++];
|
||||
|
||||
data.radius[iatoms] = buf[m++];
|
||||
data.rmass[iatoms] = buf[m++];
|
||||
if (data.radius[iatoms] == 0.0) data.density[iatoms] = data.rmass[iatoms];
|
||||
else
|
||||
data.density[iatoms] = data.rmass[iatoms] /
|
||||
(4.0*PI/3.0 *
|
||||
data.radius[iatoms]*data.radius[iatoms]*data.radius[iatoms]);
|
||||
data.omegax[iatoms] = buf[m++];
|
||||
data.omegay[iatoms] = buf[m++];
|
||||
data.omegaz[iatoms] = buf[m++];
|
||||
|
||||
return m;
|
||||
}
|
||||
|
||||
int atom_tri(double *buf, Data &data, int iatoms)
|
||||
{
|
||||
fprintf(stderr,"support for atom style tri is not fully implemented\n");
|
||||
exit(1);
|
||||
}
|
||||
|
||||
int atom_wavepacket(double *buf, Data &data, int iatoms)
|
||||
{
|
||||
fprintf(stderr,"support for atom style wavepacket is not fully implemented\n");
|
||||
exit(1);
|
||||
}
|
||||
|
||||
// ---------------------------------------------------------------------
|
||||
// per-atom memory allocation routines
|
||||
// one routine per atom style
|
||||
|
|
@ -1236,6 +1320,7 @@ void allocate_dipole(Data &data)
|
|||
data.mux = new double[data.natoms];
|
||||
data.muy = new double[data.natoms];
|
||||
data.muz = new double[data.natoms];
|
||||
data.mul = new double[data.natoms];
|
||||
}
|
||||
|
||||
void allocate_full(Data &data)
|
||||
|
|
@ -1320,6 +1405,30 @@ void allocate_peri(Data &data)
|
|||
data.x0z = new double[data.natoms];
|
||||
}
|
||||
|
||||
void allocate_line(Data &data)
|
||||
{
|
||||
fprintf(stderr,"support for atom style line is not fully implemented\n");
|
||||
exit(1);
|
||||
}
|
||||
|
||||
void allocate_meso(Data &data)
|
||||
{
|
||||
fprintf(stderr,"support for atom style meso is not fully implemented\n");
|
||||
exit(1);
|
||||
}
|
||||
|
||||
void allocate_tri(Data &data)
|
||||
{
|
||||
fprintf(stderr,"support for atom style tri is not fully implemented\n");
|
||||
exit(1);
|
||||
}
|
||||
|
||||
void allocate_wavepacket(Data &data)
|
||||
{
|
||||
fprintf(stderr,"support for atom style wavepacket is not fully implemented\n");
|
||||
exit(1);
|
||||
}
|
||||
|
||||
// ---------------------------------------------------------------------
|
||||
// pair coeffs
|
||||
// one section for each pair style
|
||||
|
|
@ -1610,6 +1719,39 @@ void pair(FILE *fp, Data &data, char *style, int flag)
|
|||
}
|
||||
}
|
||||
|
||||
} else if (strcmp(style,"dipole/sf") == 0) {
|
||||
|
||||
double cut_lj_global = read_double(fp);
|
||||
double cut_coul_global = read_double(fp);
|
||||
int mix_flag = read_int(fp);
|
||||
|
||||
if (!flag) return;
|
||||
|
||||
data.pair_dipole_epsilon = new double[data.ntypes+1];
|
||||
data.pair_dipole_sigma = new double[data.ntypes+1];
|
||||
|
||||
for (i = 1; i <= data.ntypes; i++)
|
||||
for (j = i; j <= data.ntypes; j++) {
|
||||
itmp = read_int(fp);
|
||||
if (i == j && itmp == 0) {
|
||||
printf("ERROR: Pair coeff %d,%d is not in restart file\n",i,j);
|
||||
exit(1);
|
||||
}
|
||||
if (itmp) {
|
||||
if (i == j) {
|
||||
data.pair_dipole_epsilon[i] = read_double(fp);
|
||||
data.pair_dipole_sigma[i] = read_double(fp);
|
||||
double cut_lj = read_double(fp);
|
||||
double cut_coul = read_double(fp);
|
||||
} else {
|
||||
double dipole_epsilon = read_double(fp);
|
||||
double dipole_sigma = read_double(fp);
|
||||
double cut_lj = read_double(fp);
|
||||
double cut_coul = read_double(fp);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
} else if (strcmp(style,"dpd") == 0) {
|
||||
|
||||
double temperature = read_double(fp);
|
||||
|
|
@ -2643,6 +2785,13 @@ void angle(FILE *fp, Data &data)
|
|||
fread(&data.angle_cosine_squared_theta0[1],
|
||||
sizeof(double),data.nangletypes,fp);
|
||||
|
||||
} else if (strcmp(data.angle_style,"dipole") == 0) {
|
||||
|
||||
data.angle_harmonic_k = new double[data.nangletypes+1];
|
||||
data.angle_harmonic_theta0 = new double[data.nangletypes+1];
|
||||
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,"harmonic") == 0) {
|
||||
|
||||
data.angle_harmonic_k = new double[data.nangletypes+1];
|
||||
|
|
@ -2994,7 +3143,7 @@ void Data::stats()
|
|||
// write the data file and input file
|
||||
// ---------------------------------------------------------------------
|
||||
|
||||
void Data::write(FILE *fp, FILE *fp2)
|
||||
void Data::write(FILE *fp, FILE *fp2, int write_coeffs, int write_vels)
|
||||
{
|
||||
fprintf(fp,"LAMMPS data file from restart file: timestep = "
|
||||
BIGINT_FORMAT ", procs = %d\n\n",ntimestep,nprocs);
|
||||
|
|
@ -3053,7 +3202,7 @@ void Data::write(FILE *fp, FILE *fp2)
|
|||
|
||||
// pair coeffs to data file
|
||||
|
||||
if (pair_style && fp2 == NULL) {
|
||||
if (write_coeffs && pair_style && fp2 == NULL) {
|
||||
if ((strcmp(pair_style,"none") != 0) &&
|
||||
(strcmp(pair_style,"adp") != 0) &&
|
||||
(strcmp(pair_style,"airebo") != 0) &&
|
||||
|
|
@ -3108,7 +3257,8 @@ void Data::write(FILE *fp, FILE *fp2)
|
|||
pair_colloid_A12[i],pair_colloid_sigma[i],
|
||||
pair_colloid_d2[i],pair_colloid_d2[i]);
|
||||
|
||||
} else if (strcmp(pair_style,"dipole/cut") == 0) {
|
||||
} else if ((strcmp(pair_style,"dipole/cut") == 0) ||
|
||||
(strcmp(pair_style,"dipole/sf") == 0)) {
|
||||
for (int i = 1; i <= ntypes; i++)
|
||||
fprintf(fp,"%d %g %g\n",i,
|
||||
pair_dipole_epsilon[i],pair_dipole_sigma[i]);
|
||||
|
|
@ -3203,7 +3353,7 @@ void Data::write(FILE *fp, FILE *fp2)
|
|||
// pair coeffs to input file
|
||||
// only supported styles = cg/cmm
|
||||
|
||||
if (pair_style && fp2) {
|
||||
if (write_coeffs && pair_style && fp2) {
|
||||
if ((strcmp(pair_style,"lj/sdk") == 0) ||
|
||||
(strcmp(pair_style,"lj/sdk/coul/long") == 0) ||
|
||||
(strcmp(pair_style,"cg/cmm") == 0) ||
|
||||
|
|
@ -3228,7 +3378,7 @@ void Data::write(FILE *fp, FILE *fp2)
|
|||
|
||||
// bond coeffs to data file
|
||||
|
||||
if (bond_style && fp2 == NULL) {
|
||||
if (write_coeffs && bond_style && fp2 == NULL) {
|
||||
if ((strcmp(bond_style,"none") != 0) &&
|
||||
(strcmp(bond_style,"table") != 0) &&
|
||||
(strcmp(bond_style,"hybrid") != 0))
|
||||
|
|
@ -3292,7 +3442,7 @@ void Data::write(FILE *fp, FILE *fp2)
|
|||
// bond coeffs to input file
|
||||
// only supported styles = harmonic
|
||||
|
||||
if (bond_style && fp2) {
|
||||
if (write_coeffs && bond_style && fp2) {
|
||||
if (strcmp(bond_style,"harmonic") == 0) {
|
||||
for (int i = 1; i <= nbondtypes; i++)
|
||||
fprintf(fp2,"bond_coeff %d %g %g\n",i,
|
||||
|
|
@ -3307,7 +3457,7 @@ void Data::write(FILE *fp, FILE *fp2)
|
|||
|
||||
// angle coeffs to data file
|
||||
|
||||
if (angle_style && fp2 == NULL) {
|
||||
if (write_coeffs && angle_style && fp2 == NULL) {
|
||||
if ((strcmp(angle_style,"none") != 0) &&
|
||||
(strcmp(angle_style,"table") != 0) &&
|
||||
(strcmp(angle_style,"hybrid") != 0))
|
||||
|
|
@ -3359,6 +3509,11 @@ void Data::write(FILE *fp, FILE *fp2)
|
|||
angle_cosine_squared_k[i],
|
||||
angle_cosine_squared_theta0[i]/PI*180.0);
|
||||
|
||||
} else if (strcmp(angle_style,"dipole") == 0) {
|
||||
for (int i = 1; i <= nangletypes; i++)
|
||||
fprintf(fp,"%d %g %g\n",i,
|
||||
angle_harmonic_k[i],angle_harmonic_theta0[i]/PI*180.0);
|
||||
|
||||
} else if (strcmp(angle_style,"harmonic") == 0) {
|
||||
for (int i = 1; i <= nangletypes; i++)
|
||||
fprintf(fp,"%d %g %g\n",i,
|
||||
|
|
@ -3382,7 +3537,7 @@ void Data::write(FILE *fp, FILE *fp2)
|
|||
// angle coeffs to input file
|
||||
// only supported styles = cosine/squared, harmonic, cg/cmm
|
||||
|
||||
if (angle_style && fp2) {
|
||||
if (write_coeffs && angle_style && fp2) {
|
||||
if ((strcmp(angle_style,"cosine/squared") == 0) ||
|
||||
(strcmp(angle_style,"cosine/delta") == 0)) {
|
||||
for (int i = 1; i <= nangletypes; i++)
|
||||
|
|
@ -3415,7 +3570,7 @@ void Data::write(FILE *fp, FILE *fp2)
|
|||
}
|
||||
}
|
||||
|
||||
if (dihedral_style) {
|
||||
if (write_coeffs && dihedral_style) {
|
||||
if ((strcmp(dihedral_style,"none") != 0) &&
|
||||
(strcmp(dihedral_style,"table") != 0) &&
|
||||
(strcmp(dihedral_style,"hybrid") != 0))
|
||||
|
|
@ -3510,7 +3665,7 @@ void Data::write(FILE *fp, FILE *fp2)
|
|||
}
|
||||
}
|
||||
|
||||
if (improper_style) {
|
||||
if (write_coeffs && improper_style) {
|
||||
if ((strcmp(improper_style,"none") != 0) &&
|
||||
(strcmp(improper_style,"hybrid") != 0))
|
||||
fprintf(fp,"\nImproper Coeffs\n\n");
|
||||
|
|
@ -3560,9 +3715,13 @@ void Data::write(FILE *fp, FILE *fp2)
|
|||
if (style_dipole) write_atom_dipole(fp,i,ix,iy,iz);
|
||||
if (style_ellipsoid) write_atom_ellipsoid(fp,i,ix,iy,iz);
|
||||
if (style_full) write_atom_full(fp,i,ix,iy,iz);
|
||||
if (style_sphere) write_atom_sphere(fp,i,ix,iy,iz);
|
||||
if (style_line) write_atom_line(fp,i,ix,iy,iz);
|
||||
if (style_meso) write_atom_meso(fp,i,ix,iy,iz);
|
||||
if (style_molecular) write_atom_molecular(fp,i,ix,iy,iz);
|
||||
if (style_peri) write_atom_peri(fp,i,ix,iy,iz);
|
||||
if (style_sphere) write_atom_sphere(fp,i,ix,iy,iz);
|
||||
if (style_tri) write_atom_tri(fp,i,ix,iy,iz);
|
||||
if (style_wavepacket) write_atom_wavepacket(fp,i,ix,iy,iz);
|
||||
fprintf(fp,"\n");
|
||||
|
||||
} else {
|
||||
|
|
@ -3576,16 +3735,20 @@ void Data::write(FILE *fp, FILE *fp2)
|
|||
if (k == style_dipole) write_atom_dipole_extra(fp,i);
|
||||
if (k == style_ellipsoid) write_atom_ellipsoid_extra(fp,i);
|
||||
if (k == style_full) write_atom_full_extra(fp,i);
|
||||
if (k == style_sphere) write_atom_sphere_extra(fp,i);
|
||||
if (k == style_line) write_atom_line_extra(fp,i);
|
||||
if (k == style_meso) write_atom_meso_extra(fp,i);
|
||||
if (k == style_molecular) write_atom_molecular_extra(fp,i);
|
||||
if (k == style_peri) write_atom_peri_extra(fp,i);
|
||||
if (k == style_sphere) write_atom_sphere_extra(fp,i);
|
||||
if (k == style_tri) write_atom_tri_extra(fp,i);
|
||||
if (k == style_wavepacket) write_atom_wavepacket_extra(fp,i);
|
||||
}
|
||||
fprintf(fp," %d %d %d\n",ix,iy,iz);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
if (natoms) {
|
||||
if (write_vels && natoms) {
|
||||
fprintf(fp,"\nVelocities\n\n");
|
||||
for (bigint i = 0; i < natoms; i++)
|
||||
|
||||
|
|
@ -3597,9 +3760,13 @@ void Data::write(FILE *fp, FILE *fp2)
|
|||
if (style_dipole) write_vel_dipole(fp,i);
|
||||
if (style_ellipsoid) write_vel_ellipsoid(fp,i);
|
||||
if (style_full) write_vel_full(fp,i);
|
||||
if (style_sphere) write_vel_sphere(fp,i);
|
||||
if (style_line) write_vel_line(fp,i);
|
||||
if (style_meso) write_vel_meso(fp,i);
|
||||
if (style_molecular) write_vel_molecular(fp,i);
|
||||
if (style_peri) write_vel_peri(fp,i);
|
||||
if (style_sphere) write_vel_sphere(fp,i);
|
||||
if (style_tri) write_vel_tri(fp,i);
|
||||
if (style_wavepacket) write_vel_wavepacket(fp,i);
|
||||
fprintf(fp,"\n");
|
||||
|
||||
} else {
|
||||
|
|
@ -3612,9 +3779,13 @@ void Data::write(FILE *fp, FILE *fp2)
|
|||
if (k == style_dipole) write_vel_dipole_extra(fp,i);
|
||||
if (k == style_ellipsoid) write_vel_ellipsoid_extra(fp,i);
|
||||
if (k == style_full) write_vel_full_extra(fp,i);
|
||||
if (k == style_sphere) write_vel_sphere_extra(fp,i);
|
||||
if (k == style_line) write_vel_line_extra(fp,i);
|
||||
if (k == style_meso) write_vel_meso_extra(fp,i);
|
||||
if (k == style_molecular) write_vel_molecular_extra(fp,i);
|
||||
if (k == style_peri) write_vel_peri_extra(fp,i);
|
||||
if (k == style_sphere) write_vel_sphere_extra(fp,i);
|
||||
if (k == style_tri) write_vel_tri_extra(fp,i);
|
||||
if (k == style_wavepacket) write_vel_wavepacket_extra(fp,i);
|
||||
}
|
||||
fprintf(fp,"\n");
|
||||
}
|
||||
|
|
@ -3696,7 +3867,8 @@ void Data::write_atom_dipole(FILE *fp, int i, int ix, int iy, int iz)
|
|||
fprintf(fp,"%d %d %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e "
|
||||
"%-1.16e %-1.16e %d %d %d",
|
||||
tag[i],type[i],q[i],x[i],y[i],z[i],
|
||||
mux[i],muy[i],muz[i],ix,iy,iz);
|
||||
mul[i]*mux[i],mul[i]*muy[i],mul[i]*muz[i],
|
||||
ix,iy,iz);
|
||||
}
|
||||
|
||||
void Data::write_atom_ellipsoid(FILE *fp, int i, int ix, int iy, int iz)
|
||||
|
|
@ -3711,10 +3883,16 @@ void Data::write_atom_full(FILE *fp, int i, int ix, int iy, int iz)
|
|||
tag[i],molecule[i],type[i],q[i],x[i],y[i],z[i],ix,iy,iz);
|
||||
}
|
||||
|
||||
void Data::write_atom_sphere(FILE *fp, int i, int ix, int iy, int iz)
|
||||
void Data::write_atom_line(FILE *fp, int i, int ix, int iy, int iz)
|
||||
{
|
||||
fprintf(fp,"%d %d %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e %d %d %d",
|
||||
tag[i],type[i],2.0*radius[i],density[i],x[i],y[i],z[i],ix,iy,iz);
|
||||
fprintf(stderr,"support for atom style line is not yet complete\n");
|
||||
exit(1);
|
||||
}
|
||||
|
||||
void Data::write_atom_meso(FILE *fp, int i, int ix, int iy, int iz)
|
||||
{
|
||||
fprintf(stderr,"support for atom style meso is not yet complete\n");
|
||||
exit(1);
|
||||
}
|
||||
|
||||
void Data::write_atom_molecular(FILE *fp, int i, int ix, int iy, int iz)
|
||||
|
|
@ -3729,6 +3907,24 @@ void Data::write_atom_peri(FILE *fp, int i, int ix, int iy, int iz)
|
|||
tag[i],type[i],vfrac[i],rmass[i],x[i],y[i],z[i],ix,iy,iz);
|
||||
}
|
||||
|
||||
void Data::write_atom_sphere(FILE *fp, int i, int ix, int iy, int iz)
|
||||
{
|
||||
fprintf(fp,"%d %d %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e %d %d %d",
|
||||
tag[i],type[i],2.0*radius[i],density[i],x[i],y[i],z[i],ix,iy,iz);
|
||||
}
|
||||
|
||||
void Data::write_atom_tri(FILE *fp, int i, int ix, int iy, int iz)
|
||||
{
|
||||
fprintf(stderr,"support for atom style tri is not yet complete\n");
|
||||
exit(1);
|
||||
}
|
||||
|
||||
void Data::write_atom_wavepacket(FILE *fp, int i, int ix, int iy, int iz)
|
||||
{
|
||||
fprintf(stderr,"support for atom style wavepacket is not yet complete\n");
|
||||
exit(1);
|
||||
}
|
||||
|
||||
// ---------------------------------------------------------------------
|
||||
// per-atom write routines of extra quantities unique to style
|
||||
// one routine per atom style
|
||||
|
|
@ -3753,7 +3949,8 @@ void Data::write_atom_charge_extra(FILE *fp, int i)
|
|||
|
||||
void Data::write_atom_dipole_extra(FILE *fp, int i)
|
||||
{
|
||||
fprintf(fp," %-1.16e %-1.16e %-1.16e %-1.16e",q[i],mux[i],muy[i],muz[i]);
|
||||
fprintf(fp," %-1.16e %-1.16e %-1.16e %-1.16e",q[i],
|
||||
mul[i]*mux[i],mul[i]*muy[i],mul[i]*muz[i]);
|
||||
}
|
||||
|
||||
void Data::write_atom_ellipsoid_extra(FILE *fp, int i)
|
||||
|
|
@ -3766,9 +3963,16 @@ void Data::write_atom_full_extra(FILE *fp, int i)
|
|||
fprintf(fp," %d %-1.16e",molecule[i],q[i]);
|
||||
}
|
||||
|
||||
void Data::write_atom_sphere_extra(FILE *fp, int i)
|
||||
void Data::write_atom_line_extra(FILE *fp, int i)
|
||||
{
|
||||
fprintf(fp," %-1.16e %-1.16e",2.0*radius[i],density[i]);
|
||||
fprintf(stderr,"support for atom style line is not yet complete\n");
|
||||
exit(1);
|
||||
}
|
||||
|
||||
void Data::write_atom_meso_extra(FILE *fp, int i)
|
||||
{
|
||||
fprintf(stderr,"support for atom style meso is not yet complete\n");
|
||||
exit(1);
|
||||
}
|
||||
|
||||
void Data::write_atom_molecular_extra(FILE *fp, int i)
|
||||
|
|
@ -3781,6 +3985,23 @@ void Data::write_atom_peri_extra(FILE *fp, int i)
|
|||
fprintf(fp," %-1.16e %-1.16e",vfrac[i],rmass[i]);
|
||||
}
|
||||
|
||||
void Data::write_atom_sphere_extra(FILE *fp, int i)
|
||||
{
|
||||
fprintf(fp," %-1.16e %-1.16e",2.0*radius[i],density[i]);
|
||||
}
|
||||
|
||||
void Data::write_atom_tri_extra(FILE *fp, int i)
|
||||
{
|
||||
fprintf(stderr,"support for atom style tri is not yet complete\n");
|
||||
exit(1);
|
||||
}
|
||||
|
||||
void Data::write_atom_wavepacket_extra(FILE *fp, int i)
|
||||
{
|
||||
fprintf(stderr,"support for atom style wavepacket is not yet complete\n");
|
||||
exit(1);
|
||||
}
|
||||
|
||||
// ---------------------------------------------------------------------
|
||||
// per-atom velocity write routines
|
||||
// one routine per atom style
|
||||
|
|
@ -3822,10 +4043,16 @@ void Data::write_vel_full(FILE *fp, int i)
|
|||
fprintf(fp,"%d %-1.16e %-1.16e %-1.16e",tag[i],vx[i],vy[i],vz[i]);
|
||||
}
|
||||
|
||||
void Data::write_vel_sphere(FILE *fp, int i)
|
||||
void Data::write_vel_line(FILE *fp, int i)
|
||||
{
|
||||
fprintf(fp,"%d %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e",
|
||||
tag[i],vx[i],vy[i],vz[i],omegax[i],omegay[i],omegaz[i]);
|
||||
fprintf(stderr,"support for atom style line is not yet complete\n");
|
||||
exit(1);
|
||||
}
|
||||
|
||||
void Data::write_vel_meso(FILE *fp, int i)
|
||||
{
|
||||
fprintf(stderr,"support for atom style meso is not yet complete\n");
|
||||
exit(1);
|
||||
}
|
||||
|
||||
void Data::write_vel_molecular(FILE *fp, int i)
|
||||
|
|
@ -3838,6 +4065,24 @@ void Data::write_vel_peri(FILE *fp, int i)
|
|||
fprintf(fp,"%d %-1.16e %-1.16e %-1.16e",tag[i],vx[i],vy[i],vz[i]);
|
||||
}
|
||||
|
||||
void Data::write_vel_sphere(FILE *fp, int i)
|
||||
{
|
||||
fprintf(fp,"%d %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e",
|
||||
tag[i],vx[i],vy[i],vz[i],omegax[i],omegay[i],omegaz[i]);
|
||||
}
|
||||
|
||||
void Data::write_vel_tri(FILE *fp, int i)
|
||||
{
|
||||
fprintf(stderr,"support for atom style tri is not yet complete\n");
|
||||
exit(1);
|
||||
}
|
||||
|
||||
void Data::write_vel_wavepacket(FILE *fp, int i)
|
||||
{
|
||||
fprintf(stderr,"support for atom style wavepacket is not yet complete\n");
|
||||
exit(1);
|
||||
}
|
||||
|
||||
// ---------------------------------------------------------------------
|
||||
// per-atom velocity write routines of extra quantities unique to style
|
||||
// one routine per atom style
|
||||
|
|
@ -3855,14 +4100,18 @@ void Data::write_vel_ellipsoid_extra(FILE *fp, int i)
|
|||
}
|
||||
|
||||
void Data::write_vel_full_extra(FILE *fp, int i) {}
|
||||
void Data::write_vel_line_extra(FILE *fp, int i) {}
|
||||
void Data::write_vel_meso_extra(FILE *fp, int i) {}
|
||||
|
||||
void Data::write_vel_molecular_extra(FILE *fp, int i) {}
|
||||
void Data::write_vel_peri_extra(FILE *fp, int i) {}
|
||||
void Data::write_vel_sphere_extra(FILE *fp, int i)
|
||||
{
|
||||
fprintf(fp," %-1.16e %-1.16e %-1.16e",omegax[i],omegay[i],omegaz[i]);
|
||||
}
|
||||
void Data::write_vel_tri_extra(FILE *fp, int i) {}
|
||||
void Data::write_vel_wavepacket_extra(FILE *fp, int i) {}
|
||||
|
||||
void Data::write_vel_molecular_extra(FILE *fp, int i) {}
|
||||
void Data::write_vel_peri_extra(FILE *fp, int i) {}
|
||||
|
||||
// ---------------------------------------------------------------------
|
||||
// strip known accelerator suffixes from style name
|
||||
|
|
|
|||
Loading…
Reference in New Issue