double maxwell_velocitiesC(int part_id, int N_T) {
double v[3], v_av[3],uniran[2];
int i;
int flag=1;
uniran[0]=d_random();
uniran[1]=d_random();
v_av[0] = v_av[1] = v_av[2] = 0.0;
for (i=part_id; i < part_id+N_T; i++) {
if(flag == 1 ) {
v[0] = pow((-2. * log(uniran[0])),0.5) * cos (2. * PI * uniran[1]) * time_step;
v[1] = pow((-2. * log(uniran[1])),0.5) * sin (2. * PI * uniran[0]) * time_step;
uniran[0]=d_random();
uniran[1]=d_random();
v[2] = pow((-2. * log(uniran[0])),0.5) * cos (2. * PI * uniran[1]) * time_step;
flag = 0;
} else {
v[0] = pow((-2. * log(uniran[1])),0.5) * sin (2. * PI * uniran[0]) * time_step;
uniran[0]=d_random();
uniran[1]=d_random();
v[1] = pow((-2. * log(uniran[0])),0.5) * cos (2. * PI * uniran[1]) * time_step;
v[2] = pow((-2. * log(uniran[1])),0.5) * sin (2. * PI * uniran[0]) * time_step;
flag = 1;
}
//printf("%f \n %f \n %f \n",v[0],v[1],v[2]);
v_av[0]+=v[0]; v_av[1]+=v[1]; v_av[2]+=v[2];
if (set_particle_v(i, v)==ES_ERROR) {
fprintf(stderr, "INTERNAL ERROR: failed upon setting one of the velocities in Espresso (current average: %f)!\n",sqrt(SQR(v_av[0])+SQR(v_av[1])+SQR(v_av[2])));
fprintf(stderr, "Aborting...\n"); errexit();
}
}
// note that time_step == -1, as long as it is not yet set
return ( sqrt(SQR(v_av[0])+SQR(v_av[1])+SQR(v_av[2])) / fabs(time_step) );
}
double velocitiesC(double v_max, int part_id, int N_T) {
double v[3], v_av[3];
int i;
v_av[0] = v_av[1] = v_av[2] = 0.0;
for (i=part_id; i < part_id+N_T; i++) {
do {
v[0] = v_max * 2.*(d_random()-.5) * time_step;
v[1] = v_max * 2.*(d_random()-.5) * time_step;
v[2] = v_max * 2.*(d_random()-.5) * time_step;
// note that time_step == -1, as long as it is not yet set
} while ( sqrt(SQR(v[0])+SQR(v[1])+SQR(v[2])) > v_max * fabs(time_step));
v_av[0]+=v[0]; v_av[1]+=v[1]; v_av[2]+=v[2];
if (set_particle_v(i, v)==ES_ERROR) {
fprintf(stderr, "INTERNAL ERROR: failed upon setting one of the velocities in Espresso (current average: %f)!\n",
sqrt(SQR(v_av[0])+SQR(v_av[1])+SQR(v_av[2])));
fprintf(stderr, "Aborting...\n"); errexit();
}
}
// note that time_step == -1, as long as it is not yet set
return ( sqrt(SQR(v_av[0])+SQR(v_av[1])+SQR(v_av[2])) / fabs(time_step) );
}
int tclcommand_readmd(ClientData dummy, Tcl_Interp *interp,
int argc, char **argv)
{
char *row;
int pos_row[3] = { -1 }, v_row[3] = { -1 },
#ifdef DIPOLES
dip_row[3] = { -1 },
#endif
f_row[3] = { -1 };
int av_pos = 0, av_v = 0,
#ifdef DIPOLES
av_dip=0,
#endif
#ifdef MASS
av_mass=0,
#endif
#ifdef SHANCHEN
av_solvation=0,
#endif
av_f = 0,
#ifdef ELECTROSTATICS
av_q = 0,
#endif
av_type = 0;
int node, i;
struct MDHeader header;
Particle data;
int tcl_file_mode;
Tcl_Channel channel;
if (argc != 2) {
Tcl_AppendResult(interp, "wrong # args: should be \"",
argv[0], " <file>\"",
(char *) NULL);
return (TCL_ERROR);
}
if ((channel = Tcl_GetChannel(interp, argv[1], &tcl_file_mode)) == NULL)
return (TCL_ERROR);
/* tune channel to binary translation, e.g. none */
Tcl_SetChannelOption(interp, channel, "-translation", "binary");
Tcl_Read(channel, (char *)&header, sizeof(header));
/* check token */
if (strncmp(header.magic, MDMAGIC, 4) || header.n_rows < 0) {
Tcl_AppendResult(interp, "data file \"", argv[1],
"\" does not contain tcl MD data",
(char *) NULL);
return (TCL_ERROR);
}
if (!particle_node)
build_particle_node();
/* parse rows */
row = (char*)malloc(header.n_rows*sizeof(char));
for (i = 0; i < header.n_rows; i++) {
Tcl_Read(channel, (char *)&row[i], sizeof(char));
switch (row[i]) {
case POSX: pos_row[0] = i; break;
case POSY: pos_row[1] = i; break;
case POSZ: pos_row[2] = i; break;
case VX: v_row[0] = i; break;
case VY: v_row[1] = i; break;
case VZ: v_row[2] = i; break;
#ifdef DIPOLES
case MX: dip_row[0] = i; break;
case MY: dip_row[1] = i; break;
case MZ: dip_row[2] = i; break;
#endif
case FX: f_row[0] = i; break;
case FY: f_row[1] = i; break;
case FZ: f_row[2] = i; break;
#ifdef MASS
case MASSES: av_mass = 1; break;
#endif
#ifdef SHANCHEN
case SOLVATION: av_solvation = 1; break;
#endif
#ifdef ELECTROSTATICS
case Q: av_q = 1; break;
#endif
case TYPE: av_type = 1; break;
}
}
/* *_row[0] tells if * data is completely available -
* otherwise we ignore it */
if (pos_row[0] != -1 && pos_row[1] != -1 && pos_row[2] != -1) {
av_pos = 1;
}
if (v_row[0] != -1 && v_row[1] != -1 && v_row[2] != -1) {
av_v = 1;
}
if (f_row[0] != -1 && f_row[1] != -1 && f_row[2] != -1) {
av_f = 1;
}
#ifdef DIPOLES
if (dip_row[0] != -1 && dip_row[1] != -1 && dip_row[2] != -1) {
av_dip = 1;
}
#endif
while (!Tcl_Eof(channel)) {
Tcl_Read(channel, (char *)&data.p.identity, sizeof(int));
if (data.p.identity == -1)
break;
/* printf("id=%d\n", data.identity); */
if (data.p.identity < 0) {
Tcl_AppendResult(interp, "illegal data format in data file \"", argv[1],
"\", perhaps wrong file?",
(char *) NULL);
free(row);
return (TCL_ERROR);
}
for (i = 0; i < header.n_rows; i++) {
switch (row[i]) {
case POSX: Tcl_Read(channel, (char *)&data.r.p[0], sizeof(double)); break;
case POSY: Tcl_Read(channel, (char *)&data.r.p[1], sizeof(double)); break;
case POSZ: Tcl_Read(channel, (char *)&data.r.p[2], sizeof(double)); break;
case VX: Tcl_Read(channel, (char *)&data.m.v[0], sizeof(double)); break;
case VY: Tcl_Read(channel, (char *)&data.m.v[1], sizeof(double)); break;
case VZ: Tcl_Read(channel, (char *)&data.m.v[2], sizeof(double)); break;
case FX: Tcl_Read(channel, (char *)&data.f.f[0], sizeof(double)); break;
case FY: Tcl_Read(channel, (char *)&data.f.f[1], sizeof(double)); break;
case FZ: Tcl_Read(channel, (char *)&data.f.f[2], sizeof(double)); break;
case MASSES:
#ifdef MASS
Tcl_Read(channel, (char *)&data.p.mass, sizeof(double)); break;
#else
{
double dummy_mass;
Tcl_Read(channel, (char *)&dummy_mass, sizeof(double)); break;
}
#endif
#ifdef ELECTROSTATICS
case Q: Tcl_Read(channel, (char *)&data.p.q, sizeof(double)); break;
#endif
#ifdef DIPOLES
case MX: Tcl_Read(channel, (char *)&data.r.dip[0], sizeof(double)); break;
case MY: Tcl_Read(channel, (char *)&data.r.dip[1], sizeof(double)); break;
case MZ: Tcl_Read(channel, (char *)&data.r.dip[2], sizeof(double)); break;
#endif
case TYPE: Tcl_Read(channel, (char *)&data.p.type, sizeof(int)); break;
}
}
node = (data.p.identity <= max_seen_particle) ? particle_node[data.p.identity] : -1;
if (node == -1) {
if (!av_pos) {
Tcl_AppendResult(interp, "new particle without position data",
(char *) NULL);
free(row);
return (TCL_ERROR);
}
}
if (av_pos)
place_particle(data.p.identity, data.r.p);
#ifdef MASS
if (av_mass)
set_particle_mass(data.p.identity, data.p.mass);
#endif
#ifdef SHANCHEN
if (av_solvation)
set_particle_solvation(data.p.identity, data.p.solvation);
#endif
#ifdef ELECTROSTATICS
if (av_q)
set_particle_q(data.p.identity, data.p.q);
#endif
#ifdef DIPOLES
if (av_dip)
set_particle_dip(data.p.identity, data.r.dip);
#endif
if (av_v)
set_particle_v(data.p.identity, data.m.v);
if (av_f)
set_particle_f(data.p.identity, data.f.f);
if (av_type)
set_particle_type(data.p.identity, data.p.type);
}
free(row);
return TCL_OK;
}
