void analyze_activate(int ind) {
int i;
double pos[3];
n_part_conf = n_part;
for(i=0; i<n_part_conf; i++) {
pos[0] = configs[ind][3*i];
pos[1] = configs[ind][3*i+1];
pos[2] = configs[ind][3*i+2];
if (place_particle(i, pos)==ES_ERROR) {
runtimeErrorMsg() <<"failed upon replacing particle " << i << " in Espresso";
}
}
}
void analyze_activate(int ind) {
int i;
double pos[3];
n_part_conf = n_part;
for(i=0; i<n_part_conf; i++) {
pos[0] = configs[ind][3*i];
pos[1] = configs[ind][3*i+1];
pos[2] = configs[ind][3*i+2];
if (place_particle(i, pos)==ES_ERROR) {
char *errtxt = runtime_error(128 + ES_INTEGER_SPACE);
ERROR_SPRINTF(errtxt, "{057 failed upon replacing particle %d in Espresso} ", i);
}
}
}
int counterionsC(int N_CI, int part_id, int mode, double shield, int max_try, double val_CI, int type_CI) {
int n, cnt1,max_cnt;
double pos[3];
cnt1 = max_cnt = 0;
for (n=0; n<N_CI; n++) {
for (cnt1=0; cnt1<max_try; cnt1++) {
pos[0]=box_l[0]*d_random();
pos[1]=box_l[1]*d_random();
pos[2]=box_l[2]*d_random();
if ((mode!=0) || (collision(pos, shield, 0, NULL)==0)) break;
POLY_TRACE(printf("c"); fflush(NULL));
}
if (cnt1 >= max_try) return (-1);
if (place_particle(part_id, pos)==ES_PART_ERROR) return (-3);
if (set_particle_q(part_id, val_CI)==ES_ERROR) return (-3);
if (set_particle_type(part_id, type_CI)==ES_ERROR) return (-3);
part_id++; max_cnt=imax(cnt1, max_cnt);
POLY_TRACE(printf("C"); fflush(NULL));
}
POLY_TRACE(printf(" %d->%d \n",cnt1,max_cnt));
if (cnt1 >= max_try) return(-1);
return(imax(max_cnt,cnt1));
}
// Handle the collisions stored in the queue
void handle_collisions ()
{
// If we don't have virtual_sites_relative, only bonds between centers of
// colliding particles are possible and nothing is to be done here
#ifdef VIRTUAL_SITES_RELATIVE
// Does the user want bonds between virtual sites placed at the point of collision
if (collision_detection_mode==2)
{
// printf("number of collisions in handle collision are %d\n",number_of_collisions);
int bondG[3], i;
if (number_of_collisions > 0) {
// Go through the queue
for (i=0;i<number_of_collisions;i++) {
// printf("Handling collision of particles %d %d\n", collision_queue[i].pp1, collision_queue[i].pp2);
// fflush(stdout);
// The following lines will remove the relative velocity from
// colliding particles
// double v[3];
// for (j=0;j<3;j++)
// {
// v[j] =0.5 *((local_particles[collision_queue[i].pp1])->m.v[j] +(local_particles[collision_queue[i].pp2])->m.v[j]);
// (local_particles[collision_queue[i].pp1])->m.v[j] =v[j];
// (local_particles[collision_queue[i].pp2])->m.v[j] =v[j];
// }
// Create virtual sites and bind them together
// Virtual site related to first particle in the collision
place_particle(max_seen_particle+1,collision_queue[i].point_of_collision);
vs_relate_to(max_seen_particle,collision_queue[i].pp1);
(local_particles[max_seen_particle])->p.isVirtual=1;
(local_particles[max_seen_particle])->p.type=collision_vs_particle_type;
// Virtual particle related to 2nd particle of the collision
place_particle(max_seen_particle+1,collision_queue[i].point_of_collision);
vs_relate_to(max_seen_particle,collision_queue[i].pp2);
(local_particles[max_seen_particle])->p.isVirtual=1;
(local_particles[max_seen_particle])->p.type=collision_vs_particle_type;
switch (bonded_ia_params[collision_detection_bond_vs].num) {
case 1: {
// Create bond between the virtual particles
bondG[0] = collision_detection_bond_vs;
bondG[1] = max_seen_particle-1;
local_change_bond(max_seen_particle, bondG, 0);
break;
}
case 2: {
// Create 1st bond between the virtual particles
bondG[0] = collision_detection_bond_vs;
bondG[1] = collision_queue[i].pp1;
bondG[2] = collision_queue[i].pp2;
local_change_bond(max_seen_particle, bondG, 0);
local_change_bond(max_seen_particle-1, bondG, 0);
break;
}
}
}
}
}
#endif
// Reset the collision queue
number_of_collisions = 0;
free(collision_queue);
}
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;
}
int saltC(int N_pS, int N_nS, int part_id, int mode, double shield, int max_try, double val_pS, double val_nS, int type_pS, int type_nS, double rad) {
int n, cnt1,max_cnt;
double pos[3], dis2;
cnt1 = max_cnt = 0;
/* Place positive salt ions */
for (n=0; n<N_pS; n++) {
for (cnt1=0; cnt1<max_try; cnt1++) {
if (rad > 0.) {
pos[0]=rad*(2.*d_random()-1.);
pos[1]=rad*(2.*d_random()-1.);
pos[2]=rad*(2.*d_random()-1.);
dis2 = pos[0]*pos[0]+pos[1]*pos[1]+pos[2]*pos[2];
pos[0] += box_l[0]*0.5;
pos[1] += box_l[1]*0.5;
pos[2] += box_l[2]*0.5;
if (((mode!=0) || (collision(pos, shield, 0, NULL)==0)) && (dis2 < (rad * rad))) break;
} else {
pos[0]=box_l[0]*d_random();
pos[1]=box_l[1]*d_random();
pos[2]=box_l[2]*d_random();
if ((mode!=0) || (collision(pos, shield, 0, NULL)==0)) break;
}
POLY_TRACE(printf("p"); fflush(NULL));
}
if (cnt1 >= max_try) return (-1);
if (place_particle(part_id, pos)==ES_PART_ERROR) return (-3);
if (set_particle_q(part_id, val_pS)==ES_ERROR) return (-3);
if (set_particle_type(part_id, type_pS)==ES_ERROR) return (-3);
part_id++; max_cnt=imax(cnt1, max_cnt);
POLY_TRACE(printf("P"); fflush(NULL));
}
POLY_TRACE(printf(" %d->%d \n",cnt1,max_cnt));
if (cnt1 >= max_try) return(-1);
/* Place negative salt ions */
for (n=0; n<N_nS; n++) {
for (cnt1=0; cnt1<max_try; cnt1++) {
if (rad > 0.) {
pos[0]=rad*(2.*d_random()-1.);
pos[1]=rad*(2.*d_random()-1.);
pos[2]=rad*(2.*d_random()-1.);
dis2 = pos[0]*pos[0]+pos[1]*pos[1]+pos[2]*pos[2];
pos[0] += box_l[0]*0.5;
pos[1] += box_l[1]*0.5;
pos[2] += box_l[2]*0.5;
if (((mode!=0) || (collision(pos, shield, 0, NULL)==0)) && (dis2 < (rad * rad))) break;
} else {
pos[0]=box_l[0]*d_random();
pos[1]=box_l[1]*d_random();
pos[2]=box_l[2]*d_random();
if ((mode!=0) || (collision(pos, shield, 0, NULL)==0)) break;
}
POLY_TRACE(printf("n"); fflush(NULL));
}
if (cnt1 >= max_try) return (-1);
if (place_particle(part_id, pos)==ES_PART_ERROR) return (-3);
if (set_particle_q(part_id, val_nS)==ES_ERROR) return (-3);
if (set_particle_type(part_id, type_nS)==ES_ERROR) return (-3);
part_id++; max_cnt=imax(cnt1, max_cnt);
POLY_TRACE(printf("N"); fflush(NULL));
}
POLY_TRACE(printf(" %d->%d \n",cnt1,max_cnt));
if (cnt1 >= max_try) return(-2);
return(imax(max_cnt,cnt1));
}
int polymerC(int N_P, int MPC, double bond_length, int part_id, double *posed,
int mode, double shield, int max_try, double val_cM, int cM_dist,
int type_nM, int type_cM, int type_bond,
double angle, double angle2, double *posed2, int constr) {
int p,n, cnt1,cnt2,max_cnt, bond_size, *bond, i;
double phi,zz,rr;
double *poly;
double pos[3];
double poz[3];
double poy[3] = {0, 0, 0};
double pox[3] = {0, 0, 0};
double a[3] = {0, 0, 0};
double b[3],c[3]={0., 0., 0.},d[3];
double absc;
poly = (double*)malloc(3*MPC*sizeof(double));
bond_size = bonded_ia_params[type_bond].num;
bond = (int*)malloc(sizeof(int) * (bond_size + 1));
bond[0] = type_bond;
cnt1 = cnt2 = max_cnt = 0;
for (p=0; p < N_P; p++) {
for (cnt2=0; cnt2 < max_try; cnt2++) {
/* place start monomer */
if (posed!=NULL) {
/* if position of 1st monomer is given */
if (p > 0) {
free(posed);
posed=NULL;
} else {
pos[0]=posed[0];
pos[1]=posed[1];
pos[2]=posed[2];
}
} else {
/* randomly set position */
for (cnt1=0; cnt1<max_try; cnt1++) {
pos[0]=box_l[0]*d_random();
pos[1]=box_l[1]*d_random();
pos[2]=box_l[2]*d_random();
if ((mode==1) || (collision(pos, shield, 0, NULL)==0)) break;
POLY_TRACE(printf("s"); fflush(NULL));
}
if (cnt1 >= max_try) { free(poly); return (-1); }
}
poly[0] = pos[0]; poly[1] = pos[1]; poly[2] = pos[2];
max_cnt=imax(cnt1, max_cnt);
POLY_TRACE(printf("S"); fflush(NULL));
//POLY_TRACE(/* printf("placed Monomer 0 at (%f,%f,%f)\n",pos[0],pos[1],pos[2]) */);
poz[0]=pos[0]; poz[1]=pos[1]; poz[2]=pos[2];
/* place 2nd monomer */
n=1;
if (posed2 != NULL && posed != NULL && angle2 > -1.0) {
/* if position of 2nd monomer is given */
pos[0]=posed2[0];
pos[1]=posed2[1];
pos[2]=posed2[2];
/* calculate preceding monomer so that bond_length is correct */
absc=sqrt(SQR(pos[0]-poz[0])+SQR(pos[1]-poz[1])+SQR(pos[2]-poz[2]));
poz[0]=pos[0]+(poz[0]-pos[0])*bond_length/absc;
poz[1]=pos[1]+(poz[1]-pos[1])*bond_length/absc;
poz[2]=pos[2]+(poz[2]-pos[2])*bond_length/absc;
//POLY_TRACE(/* printf("virtually shifted position of first monomer to (%f,%f,%f)\n",poz[0],poz[1],poz[2]) */);
} else {
/* randomly place 2nd monomer */
for (cnt1=0; cnt1<max_try; cnt1++) {
zz = (2.0*d_random()-1.0)*bond_length;
rr = sqrt(SQR(bond_length)-SQR(zz));
phi = 2.0*PI*d_random();
pos[0] = poz[0]+rr*cos(phi);
pos[1] = poz[1]+rr*sin(phi);
pos[2] = poz[2]+zz;
#ifdef CONSTRAINTS
if(constr==0 || constraint_collision(pos,poly+3*(n-1))==0){
#endif
if (mode==1 || collision(pos, shield, n, poly)==0) break;
if (mode==0) { cnt1 = -1; break; }
#ifdef CONSTRAINTS
}
#endif
POLY_TRACE(printf("m"); fflush(NULL));
}
if (cnt1 >= max_try) {
fprintf(stderr,"\nWarning! Attempt #%d to build polymer %d failed while placing monomer 2!\n",cnt2+1,p);
fprintf(stderr," Retrying by re-setting the start-monomer of current chain...\n");
}
if (cnt1 == -1 || cnt1 >= max_try) {
continue; /* continue the main loop */
}
}
if(posed2!=NULL && p>0) {
free(posed2);
posed2=NULL;
}
poly[3*n] = pos[0]; poly[3*n+1] = pos[1]; poly[3*n+2] = pos[2];
max_cnt=imax(cnt1, max_cnt);
POLY_TRACE(printf("M"); fflush(NULL));
//POLY_TRACE(/* printf("placed Monomer 1 at (%f,%f,%f)\n",pos[0],pos[1],pos[2]) */);
/* place remaining monomers */
for (n=2; n<MPC; n++) {
if (angle2 > -1.0) {
if(n==2) { /* if the 2nd angle is set, construct preceding monomer
with resulting plane perpendicular on the xy-plane */
poy[0]=2*poz[0]-pos[0];
poy[1]=2*poz[1]-pos[1];
if(pos[2]==poz[2])
poy[2]=poz[2]+1;
else
poy[2]=poz[2];
} else {
/* save 3rd last monomer */
pox[0]=poy[0]; pox[1]=poy[1]; pox[2]=poy[2];
}
}
if (angle > -1.0) {
/* save one but last monomer */
poy[0]=poz[0]; poy[1]=poz[1]; poy[2]=poz[2];
}
/* save last monomer */
poz[0]=pos[0]; poz[1]=pos[1]; poz[2]=pos[2];
if(angle > -1.0){
a[0]=poy[0]-poz[0];
a[1]=poy[1]-poz[1];
a[2]=poy[2]-poz[2];
b[0]=pox[0]-poy[0];
b[1]=pox[1]-poy[1];
b[2]=pox[2]-poy[2];
vector_product(a,b,c);
}
for (cnt1=0; cnt1<max_try; cnt1++) {
if(angle > -1.0) {
if (sqrlen(c) < ROUND_ERROR_PREC) {
fprintf(stderr, "WARNING: rotation axis is 0,0,0, check the angles given to the polymer command\n");
c[0] = 1; c[1] = 0; c[2] = 0;
}
if(angle2 > -1.0 && n>2) {
vec_rotate(a,angle2,c,d);
} else {
phi = 2.0*PI*d_random();
vec_rotate(a,phi,c,d);
}
vec_rotate(d,angle,a,b);
pos[0] = poz[0] + b[0];
pos[1] = poz[1] + b[1];
pos[2] = poz[2] + b[2];
} else {
zz = (2.0*d_random()-1.0)*bond_length;
rr = sqrt(SQR(bond_length)-SQR(zz));
phi = 2.0*PI*d_random();
pos[0] = poz[0]+rr*cos(phi);
pos[1] = poz[1]+rr*sin(phi);
pos[2] = poz[2]+zz;
}
//POLY_TRACE(/* printf("a=(%f,%f,%f) absa=%f M=(%f,%f,%f) c=(%f,%f,%f) absMc=%f a*c=%f)\n",a[0],a[1],a[2],sqrt(SQR(a[0])+SQR(a[1])+SQR(a[2])),M[0],M[1],M[2],c[0],c[1],c[2],sqrt(SQR(M[0]+c[0])+SQR(M[1]+c[1])+SQR(M[2]+c[2])),a[0]*c[0]+a[1]*c[1]+a[2]*c[2]) */);
//POLY_TRACE(/* printf("placed Monomer %d at (%f,%f,%f)\n",n,pos[0],pos[1],pos[2]) */);
#ifdef CONSTRAINTS
if(constr==0 || constraint_collision(pos,poly+3*(n-1))==0){
#endif
if (mode==1 || collision(pos, shield, n, poly)==0) break;
if (mode==0) { cnt1 = -2; break; }
#ifdef CONSTRAINTS
}
#endif
POLY_TRACE(printf("m"); fflush(NULL));
}
if (cnt1 >= max_try) {
fprintf(stderr,"\nWarning! Attempt #%d to build polymer %d failed after %d unsuccessful trials to place monomer %d!\n",cnt2+1,p,cnt1,n);
fprintf(stderr," Retrying by re-setting the start-monomer of current chain...\n");
}
if (cnt1 == -2 || cnt1 >= max_try) {
n=0; break;
}
poly[3*n] = pos[0]; poly[3*n+1] = pos[1]; poly[3*n+2] = pos[2];
max_cnt=imax(cnt1, max_cnt);
POLY_TRACE(printf("M"); fflush(NULL));
}
if (n>0) break;
} /* cnt2 */
POLY_TRACE(printf(" %d/%d->%d \n",cnt1,cnt2,max_cnt));
if (cnt2 >= max_try) { free(poly); return(-2); } else max_cnt = imax(max_cnt,imax(cnt1,cnt2));
/* actually creating current polymer in ESPResSo */
for (n=0; n<MPC; n++) {
pos[0] = poly[3*n]; pos[1] = poly[3*n+1]; pos[2] = poly[3*n+2];
if (place_particle(part_id, pos)==ES_PART_ERROR ||
(set_particle_q(part_id, ((n % cM_dist==0) ? val_cM : 0.0) )==ES_ERROR) ||
(set_particle_type(part_id, ((n % cM_dist==0) ? type_cM : type_nM) )==ES_ERROR))
{ free(poly); return (-3); }
if(n>=bond_size){
bond[1] = part_id - bond_size;
for(i=2;i<=bond_size;i++){
bond[i] = part_id - bond_size + i;
}
if(change_particle_bond(part_id-bond_size+1, bond, 0)==ES_ERROR)
{ free(poly); return (-3); }
}
part_id++;
//POLY_TRACE(/* printf("placed Monomer %d at (%f,%f,%f)\n",n,pos[0],pos[1],pos[2]) */);
}
}
free(poly);
return(imax(max_cnt,cnt2));
}