void momentofinertiamatrix(int type, double *MofImatrix)
{
int i,j,count;
double p1[3],com[3],massi;
count=0;
updatePartCfg(WITHOUT_BONDS);
for(i=0;i<9;i++) MofImatrix[i]=0.;
centermass(type, com);
for (j=0; j<n_part; j++) {
if (type == partCfg[j].p.type) {
count ++;
for (i=0; i<3; i++) {
p1[i] = partCfg[j].r.p[i] - com[i];
}
massi= PMASS(partCfg[j]);
MofImatrix[0] += massi * (p1[1] * p1[1] + p1[2] * p1[2]) ;
MofImatrix[4] += massi * (p1[0] * p1[0] + p1[2] * p1[2]);
MofImatrix[8] += massi * (p1[0] * p1[0] + p1[1] * p1[1]);
MofImatrix[1] -= massi * (p1[0] * p1[1]);
MofImatrix[2] -= massi * (p1[0] * p1[2]);
MofImatrix[5] -= massi * (p1[1] * p1[2]);
}
}
/* use symmetry */
MofImatrix[3] = MofImatrix[1];
MofImatrix[6] = MofImatrix[2];
MofImatrix[7] = MofImatrix[5];
return;
}
double mindist(IntList *set1, IntList *set2)
{
double mindist, pt[3];
int i, j, in_set;
mindist = SQR(box_l[0] + box_l[1] + box_l[2]);
updatePartCfg(WITHOUT_BONDS);
for (j=0; j<n_part-1; j++) {
pt[0] = partCfg[j].r.p[0];
pt[1] = partCfg[j].r.p[1];
pt[2] = partCfg[j].r.p[2];
/* check which sets particle j belongs to
bit 0: set1, bit1: set2
*/
in_set = 0;
if (!set1 || intlist_contains(set1, partCfg[j].p.type))
in_set = 1;
if (!set2 || intlist_contains(set2, partCfg[j].p.type))
in_set |= 2;
if (in_set == 0)
continue;
for (i=j+1; i<n_part; i++)
/* accept a pair if particle j is in set1 and particle i in set2 or vice versa. */
if (((in_set & 1) && (!set2 || intlist_contains(set2, partCfg[i].p.type))) ||
((in_set & 2) && (!set1 || intlist_contains(set1, partCfg[i].p.type))))
mindist = dmin(mindist, min_distance2(pt, partCfg[i].r.p));
}
mindist = sqrt(mindist);
return mindist;
}
void nbhood(double pt[3], double r, IntList *il, int planedims[3] )
{
double d[3];
int i,j;
double r2;
r2 = r*r;
init_intlist(il);
updatePartCfg(WITHOUT_BONDS);
for (i = 0; i<n_part; i++) {
if ( (planedims[0] + planedims[1] + planedims[2]) == 3 ) {
get_mi_vector(d, pt, partCfg[i].r.p);
} else {
/* Calculate the in plane distance */
for ( j= 0 ; j < 3 ; j++ ) {
d[j] = planedims[j]*(partCfg[i].r.p[j]-pt[j]);
}
}
if (sqrlen(d) < r2) {
realloc_intlist(il, il->n + 1);
il->e[il->n] = partCfg[i].p.identity;
il->n++;
}
}
}
int updatePartCfg(int bonds_flag)
{
int j;
if(partCfg)
return 1;
partCfg = (Particle*)malloc(n_part*sizeof(Particle));
if (bonds_flag != WITH_BONDS)
mpi_get_particles(partCfg, NULL);
else
mpi_get_particles(partCfg,&partCfg_bl);
for(j=0; j<n_part; j++)
unfold_position(partCfg[j].r.p,partCfg[j].l.i);
partCfgSorted = 0;
#ifdef VIRTUAL_SITES
if (!sortPartCfg()) {
char *errtxt = runtime_error(128);
ERROR_SPRINTF(errtxt,"{094 could not sort partCfg} ");
return 0;
}
if (!updatePartCfg(bonds_flag)) {
char *errtxt = runtime_error(128);
ERROR_SPRINTF(errtxt,"{094 could not update positions of virtual sites in partcfg } ");
return 0;
}
#endif
return 1;
}
/* Get a complete list of the orientations of every lipid assuming a
bilayer structure. Requires grid*/
int get_lipid_orients(IntList* l_orient) {
int i,gi,gj, atom;
double zreflocal,zref;
double dir[3];
double refdir[3] = {0,0,1};
double grid_size[2];
double* height_grid;
if ( xdir + ydir + zdir == -3 || mode_grid_3d[xdir] <= 0 || mode_grid_3d[ydir] <= 0 ) {
char *errtxt = runtime_error(128);
ERROR_SPRINTF(errtxt,"{036 cannot calculate lipid orientations with uninitialized grid} ");
return ES_ERROR;
}
/* Allocate memory for height grid arrays and initialize these arrays */
height_grid = (double*) malloc((mode_grid_3d[xdir])*sizeof(double)*mode_grid_3d[ydir]);
/* Calculate physical size of grid mesh */
grid_size[xdir] = box_l[xdir]/(double)mode_grid_3d[xdir];
grid_size[ydir] = box_l[ydir]/(double)mode_grid_3d[ydir];
/* Update particles */
updatePartCfg(WITHOUT_BONDS);
//Make sure particles are sorted
if (!sortPartCfg()) {
fprintf(stderr,"%d,could not sort partCfg \n",this_node);
return -1;
}
if ( !calc_fluctuations(height_grid, 1) ) {
char *errtxt = runtime_error(128);
ERROR_SPRINTF(errtxt,"{034 calculation of height grid failed } ");
return -1;
}
zref = calc_zref( zdir );
for ( i = 0 ; i < n_molecules ; i++) {
atom = topology[i].part.e[0];
gi = floor( partCfg[atom].r.p[xdir]/grid_size[xdir] );
gj = floor( partCfg[atom].r.p[ydir]/grid_size[ydir] );
zreflocal = height_grid[gj+gi*mode_grid_3d[xdir]] + zref;
l_orient->e[i] = lipid_orientation(atom,partCfg,zreflocal,dir,refdir);
}
free(height_grid);
return 1;
}
int tclcommand_analyze_parse_cwvac(Tcl_Interp *interp, int argc, char **argv)
{
/* 'analyze { cwvac } <maxtau> <interval> [<chain_start> <n_chains> <chain_length>]' */
/***********************************************************************************************************/
char buffer[4*TCL_DOUBLE_SPACE+7];
int i, maxtau, interval;
double *avac, *evac;
if (argc < 2) {
Tcl_AppendResult(interp, "Wrong # of args! Usage: analyze gkmobility <maxtau> <interval> [<chain_start> <n_chains> <chain_length>]",
(char *)NULL);
return (TCL_ERROR);
} else {
if (!ARG0_IS_I(maxtau))
return (TCL_ERROR);
if (!ARG1_IS_I(interval))
return (TCL_ERROR);
argc-=2; argv+=2;
}
if (tclcommand_analyze_set_parse_chain_topology_check(interp, argc, argv) == TCL_ERROR) return TCL_ERROR;
if ((chain_n_chains == 0) || (chain_length == 0)) {
Tcl_AppendResult(interp, "The chain topology has not been set",(char *)NULL); return TCL_ERROR;
}
if (maxtau <=0) {
Tcl_AppendResult(interp, "Nothing to be done - choose <maxtau> greater zero!",(char *)NULL); return TCL_ERROR;
}
if (interval <= 0) {
Tcl_AppendResult(interp, "<interval> has to be positive", (char *)NULL);
return TCL_ERROR;
}
updatePartCfg(WITHOUT_BONDS);
analyze_cwvac(maxtau, interval, &avac, &evac);
// create return string
sprintf(buffer, "{ ");
Tcl_AppendResult(interp, buffer, (char *)NULL);
for(i=0;i<=maxtau;i++) {
sprintf(buffer,"%e ",avac[i]);
Tcl_AppendResult(interp, buffer, (char *)NULL);
}
sprintf(buffer, "} { ");
Tcl_AppendResult(interp, buffer, (char *)NULL);
for(i=0;i<=maxtau;i++) {
sprintf(buffer,"%e ",evac[i]);
Tcl_AppendResult(interp, buffer, (char *)NULL);
}
sprintf(buffer, "}");
Tcl_AppendResult(interp, buffer, (char *)NULL);
free(avac); free(evac);
return (TCL_OK);
}
int tclcommand_analyze_parse_rdfchain(Tcl_Interp *interp, int argc, char **argv)
{
/* 'analyze { rdfchain } <r_min> <r_max> <r_bins> [<chain_start> <n_chains> <chain_length>]' */
/***********************************************************************************************************/
char buffer[4*TCL_DOUBLE_SPACE+7];
int i, r_bins;
double r_min, r_max, *f1, *f2, *f3;
double bin_width, r;
if (argc < 3) {
Tcl_AppendResult(interp, "Wrong # of args! Usage: analyze rdfchain <r_min> <r_max> <r_bins> [<chain_start> <n_chains> <chain_length>]",
(char *)NULL);
return (TCL_ERROR);
} else {
if (!ARG0_IS_D(r_min))
return (TCL_ERROR);
if (!ARG1_IS_D(r_max))
return (TCL_ERROR);
if (!ARG_IS_I(2, r_bins))
return (TCL_ERROR);
argc-=3; argv+=3;
}
if (tclcommand_analyze_set_parse_chain_topology_check(interp, argc, argv) == TCL_ERROR) return TCL_ERROR;
if ((chain_n_chains == 0) || (chain_length == 0)) {
Tcl_AppendResult(interp, "The chain topology has not been set",(char *)NULL); return TCL_ERROR;
}
if (r_bins <=0) {
Tcl_AppendResult(interp, "Nothing to be done - choose <r_bins> greater zero!",(char *)NULL); return TCL_ERROR;
}
if (r_min <= 0.) {
Tcl_AppendResult(interp, "<r_min> has to be positive", (char *)NULL);
return TCL_ERROR;
}
if (r_max <= r_min) {
Tcl_AppendResult(interp, "<r_max> has to be larger than <r_min>", (char *)NULL);
return TCL_ERROR;
}
updatePartCfg(WITHOUT_BONDS);
analyze_rdfchain(r_min, r_max, r_bins, &f1, &f2, &f3);
bin_width = (r_max - r_min) / (double)r_bins;
r = r_min + bin_width/2.0;
for(i=0; i<r_bins; i++) {
sprintf(buffer,"{%f %f %f %f} ",r,f1[i],f2[i],f3[i]);
Tcl_AppendResult(interp, buffer, (char *)NULL);
r+= bin_width;
}
free(f1); free(f2); free(f3);
return (TCL_OK);
}
int tclcommand_analyze_parse_and_print_pressure_mol(Tcl_Interp *interp,int argc, char **argv)
{
char buffer[TCL_DOUBLE_SPACE];
int type1, type2;
double psum;
#ifdef ELECTROSTATICS
#ifndef INTER_RF
Tcl_ResetResult(interp);
Tcl_AppendResult(interp, "parse_and_print_pressure_mol is only possible with INTER_RF ", (char *)NULL);
return (TCL_ERROR);
#endif
#endif
updatePartCfg(WITHOUT_BONDS);
if (!sortPartCfg()) {
char *errtxt = runtime_error(128);
ERROR_SPRINTF(errtxt, "{059 parse_and_print_pressure_mol: could not sort particle config, particle ids not consecutive?} ");
return TCL_ERROR;
}
if (argc < 2) {
Tcl_ResetResult(interp);
Tcl_AppendResult(interp, "usage: analyze pressure_mol <type1> <type2>", (char *)NULL);
return (TCL_ERROR);
}
if (!ARG0_IS_I(type1)) {
Tcl_ResetResult(interp);
Tcl_AppendResult(interp, "usage: analyze pressure_mol <type1> <type2>", (char *)NULL);
return (TCL_ERROR);
}
if (!ARG1_IS_I(type2)) {
Tcl_ResetResult(interp);
Tcl_AppendResult(interp, "usage: analyze pressure_mol <type1> <type2>", (char *)NULL);
return (TCL_ERROR);
}
argc-=2;
argv+=2;
if (n_molecules==0) {
Tcl_ResetResult(interp);
Tcl_AppendResult(interp, "No molecules defined !", (char *)NULL);
return (TCL_ERROR);
}
psum=calc_pressure_mol(type1,type2);
//sprintf(buffer,"%i",type1);
//Tcl_AppendResult(interp,"{ analyze pressure_mol ",buffer," ",(char *)NULL);
//sprintf(buffer,"%i",type2);
//Tcl_AppendResult(interp,buffer," ",(char *)NULL);
sprintf(buffer,"%e",psum);
Tcl_AppendResult(interp, buffer,(char *)NULL);
return TCL_OK;
}
std::vector<double> centerofmass(int type)
{
std::vector<double> com (3);
double mass = 0.0;
updatePartCfg(WITHOUT_BONDS);
for (int i=0; i<n_part; i++) {
if ((partCfg[i].p.type == type) || (type == -1)) {
for (int j=0; j<3; j++) {
com[j] += partCfg[i].r.p[j]*(partCfg[i]).p.mass;
}
mass += (partCfg[i]).p.mass;
}
}
for (int j=0; j<3; j++) com[j] /= mass;
return com;
}
double distto(double p[3], int pid)
{
int i;
double d[3];
double mindist;
updatePartCfg(WITHOUT_BONDS);
/* larger than possible */
mindist=SQR(box_l[0] + box_l[1] + box_l[2]);
for (i=0; i<n_part; i++) {
if (pid != partCfg[i].p.identity) {
get_mi_vector(d, p, partCfg[i].r.p);
mindist = dmin(mindist, sqrlen(d));
}
}
return sqrt(mindist);
}
int tclcommand_analyze_parse_and_print_energy_kinetic_mol(Tcl_Interp *interp,int argc, char **argv)
{
char buffer[TCL_DOUBLE_SPACE];
int type;
double Ekin;
updatePartCfg(WITHOUT_BONDS);
if (!sortPartCfg()) {
char *errtxt = runtime_error(128);
ERROR_SPRINTF(errtxt, "{059 parse_and_print_energy_kinetic_mol: could not sort particle config, particle ids not consecutive?} ");
return TCL_ERROR;
}
if (argc < 1) {
Tcl_ResetResult(interp);
Tcl_AppendResult(interp, "usage: analyze energy_kinetic <type>", (char *)NULL);
return (TCL_ERROR);
}
if (!ARG0_IS_I(type)) {
Tcl_ResetResult(interp);
Tcl_AppendResult(interp, "usage: analyze energy_kinetic <type>", (char *)NULL);
return (TCL_ERROR);
}
argc-=1;
argv+=1;
if (n_molecules==0) {
Tcl_ResetResult(interp);
Tcl_AppendResult(interp, "No molecules defined !", (char *)NULL);
return (TCL_ERROR);
}
Ekin=calc_energy_kinetic_mol(type);
if (Ekin < 0.0) {
Tcl_ResetResult(interp);
sprintf(buffer,"%i",-(int)Ekin);
Tcl_AppendResult(interp,"Could not fetch com in calc_energy_kinetic_mol! From mol_id",buffer, (char *)NULL);
return (TCL_ERROR);
}
//sprintf(buffer,"%i",type);
//Tcl_AppendResult(interp,"{ analyze pressure_mol ",buffer," ",(char *)NULL);
sprintf(buffer,"%e",Ekin);
Tcl_AppendResult(interp, buffer,(char *)NULL);
return TCL_OK;
}
void centermass(int type, double *com)
{
int i, j;
double M = 0.0;
com[0]=com[1]=com[2]=0.;
updatePartCfg(WITHOUT_BONDS);
for (j=0; j<n_part; j++) {
if ((partCfg[j].p.type == type) || (type == -1)) {
for (i=0; i<3; i++) {
com[i] += partCfg[j].r.p[i]*PMASS(partCfg[j]);
}
M += PMASS(partCfg[j]);
}
}
for (i=0; i<3; i++) {
com[i] /= M;
}
return;
}
void angularmomentum(int type, double *com)
{
int i, j;
double tmp[3];
double pre_factor;
com[0]=com[1]=com[2]=0.;
updatePartCfg(WITHOUT_BONDS);
for (j=0; j<n_part; j++)
{
if (type == partCfg[j].p.type)
{
vector_product(partCfg[j].r.p,partCfg[j].m.v,tmp);
pre_factor=PMASS(partCfg[j]);
for (i=0; i<3; i++) {
com[i] += tmp[i]*pre_factor;
}
}
}
return;
}
int update_particle_array(int type) {
updatePartCfg(WITHOUT_BONDS);
if (!partCfg)
return ES_ERROR;
int t_c = 0;
for (int i=0; i<n_part; i++) {
if (partCfg[i].p.type == type ) {
type_array[Index.type[type]].id_list[t_c++] = partCfg[i].p.identity;
}
if ( t_c > (double) type_array[Index.type[type]].cur_size/2.0 ) {
if ( reallocate_type_array(type) == ES_ERROR )
return ES_ERROR;
}
}
type_array[Index.type[type]].max_entry = t_c;
for ( int i = t_c; i<type_array[Index.type[type]].cur_size; i++)
type_array[Index.type[type]].id_list[i] = -1;
return ES_OK;
}
int tclcommand_analyze_parse_and_print_check_mol(Tcl_Interp *interp,int argc, char **argv){
int j,count=0;
double dist;
char buffer[TCL_DOUBLE_SPACE];
Particle p;
updatePartCfg(WITHOUT_BONDS);
for(j=0; j<n_total_particles; j++){
if (!ifParticleIsVirtual(&partCfg[j])) continue;
get_particle_data(j,&p);
//dist=min_distance(partCfg[j].r.p,p.r.p);
unfold_position(p.r.p,p.l.i);
dist=distance(partCfg[j].r.p,p.r.p);
if (dist > 0.01){
if (count==0) Tcl_AppendResult(interp,"BEGIN Particle Missmatch: \n", (char *)NULL);
sprintf(buffer,"%i",j);
Tcl_AppendResult(interp,"Particle ",buffer, (char *)NULL);
Tcl_PrintDouble(interp,partCfg[j].r.p[0] , buffer);
Tcl_AppendResult(interp," partCfg x ",buffer, (char *)NULL);
Tcl_PrintDouble(interp,partCfg[j].r.p[1] , buffer);
Tcl_AppendResult(interp," y ",buffer, (char *)NULL);
Tcl_PrintDouble(interp,partCfg[j].r.p[2] , buffer);
Tcl_AppendResult(interp," z ",buffer, (char *)NULL);
Tcl_PrintDouble(interp,p.r.p[0] , buffer);
Tcl_AppendResult(interp," my_partCfg x ",buffer, (char *)NULL);
Tcl_PrintDouble(interp,p.r.p[1] , buffer);
Tcl_AppendResult(interp," y ",buffer, (char *)NULL);
Tcl_PrintDouble(interp,p.r.p[2] , buffer);
Tcl_AppendResult(interp," z ",buffer, (char *)NULL);
Tcl_PrintDouble(interp, dist, buffer);
Tcl_AppendResult(interp," dist ",buffer,"\n", (char *)NULL);
count++;
}
}
if (count!=0){
Tcl_AppendResult(interp,"END Particle Missmatch\n", (char *)NULL);
return(TCL_ERROR);
}
return(TCL_OK);
}
void centermass_vel(int type, double *com)
{
/*center of mass velocity scaled with time_step*/
int i, j;
int count = 0;
com[0]=com[1]=com[2]=0.;
updatePartCfg(WITHOUT_BONDS);
for (j=0; j<n_part; j++) {
if (type == partCfg[j].p.type) {
for (i=0; i<3; i++) {
com[i] += partCfg[j].m.v[i];
}
count++;
}
}
for (i=0; i<3; i++) {
com[i] /= count;
}
return;
}
std::vector<double> centerofmass_vel(int type)
{
/*center of mass velocity scaled with time_step*/
std::vector<double> com_vel (3);
int i, j;
int count = 0;
updatePartCfg(WITHOUT_BONDS);
for (j=0; j<n_part; j++) {
if (type == partCfg[j].p.type) {
for (i=0; i<3; i++) {
com_vel[i] += partCfg[j].m.v[i];
}
count++;
}
}
for (i=0; i<3; i++) {
com_vel[i] /= count;
}
return com_vel;
}
int updatePartCfg(int bonds_flag)
{
int j;
if(partCfg)
return 1;
partCfg = (Particle*)malloc(n_part*sizeof(Particle));
if (bonds_flag != WITH_BONDS)
mpi_get_particles(partCfg, NULL);
else
mpi_get_particles(partCfg,&partCfg_bl);
for(j=0; j<n_part; j++)
#ifdef LEES_EDWARDS
unfold_position(partCfg[j].r.p, partCfg[j].m.v, partCfg[j].l.i);
#else
unfold_position(partCfg[j].r.p, partCfg[j].l.i);
#endif
partCfgSorted = 0;
#ifdef VIRTUAL_SITES
if (!sortPartCfg()) {
ostringstream msg;
msg <<"could not sort partCfg";
runtimeError(msg);
return 0;
}
if (!updatePartCfg(bonds_flag)) {
ostringstream msg;
msg <<"could not update positions of virtual sites in partcfg";
runtimeError(msg);
return 0;
}
#endif
return 1;
}
int sortPartCfg()
{
int i;
Particle *sorted;
if (!partCfg)
updatePartCfg(WITHOUT_BONDS);
if (partCfgSorted)
return 1;
if (n_part != max_seen_particle + 1)
return 0;
sorted = (Particle*)malloc(n_part*sizeof(Particle));
for(i = 0; i < n_part; i++)
memcpy(&sorted[partCfg[i].p.identity], &partCfg[i], sizeof(Particle));
free(partCfg);
partCfg = sorted;
partCfgSorted = 1;
return 1;
}
int calc_radial_density_map (int xbins,int ybins,int thetabins,double xrange,double yrange, double axis[3], double center[3], IntList *beadids, DoubleList *density_map, DoubleList *density_profile) {
int i,j,t;
int pi,bi;
int nbeadtypes;
int beadcount;
double vectprod[3];
double pvector[3];
double xdist,ydist,rdist,xav,yav,theta;
double xbinwidth,ybinwidth,binvolume;
double thetabinwidth;
double *thetaradii;
int *thetacounts;
int xindex,yindex,tindex;
xbinwidth = xrange/(double)(xbins);
ybinwidth = yrange/(double)(ybins);
nbeadtypes = beadids->n;
/* Update particles */
updatePartCfg(WITHOUT_BONDS);
/*Make sure particles are folded */
for (i = 0 ; i < n_part ; i++) {
fold_coordinate(partCfg[i].r.p,partCfg[i].l.i,0);
fold_coordinate(partCfg[i].r.p,partCfg[i].l.i,1);
fold_coordinate(partCfg[i].r.p,partCfg[i].l.i,2);
}
beadcount = 0;
xav = 0.0;
yav = 0.0;
for ( pi = 0 ; pi < n_part ; pi++ ) {
for ( bi = 0 ; bi < nbeadtypes ; bi++ ) {
if ( beadids->e[bi] == partCfg[pi].p.type ) {
/* Find the vector from the point to the center */
vecsub(center,partCfg[pi].r.p,pvector);
/* Work out x and y coordinates with respect to rotation axis */
/* Find the minimum distance of the point from the axis */
vector_product(axis,pvector,vectprod);
xdist = sqrt(sqrlen(vectprod)/sqrlen(axis));
/* Find the projection of the vector from the point to the center
onto the axis vector */
ydist = scalar(axis,pvector)/sqrt(sqrlen(axis));
/* Work out relevant indices for x and y */
xindex = (int)(floor(xdist/xbinwidth));
yindex = (int)(floor((ydist+yrange*0.5)/ybinwidth));
/*
printf("x %d y %d \n",xindex,yindex);
printf("p %f %f %f \n",partCfg[pi].r.p[0],partCfg[pi].r.p[1],partCfg[pi].r.p[2]);
printf("pvec %f %f %f \n",pvector[0],pvector[1],pvector[2]);
printf("axis %f %f %f \n",axis[0],axis[1],axis[2]);
printf("dists %f %f \n",xdist,ydist);
fflush(stdout);
*/
/* Check array bounds */
if ( (xindex < xbins && xindex > 0) && (yindex < ybins && yindex > 0) ) {
density_map[bi].e[ybins*xindex+yindex] += 1;
xav += xdist;
yav += ydist;
beadcount += 1;
} else {
// fprintf(stderr,"ERROR: outside array bounds in calc_radial_density_map"); fflush(NULL); errexit();
}
}
}
}
/* Now turn counts into densities for the density map */
for ( bi = 0 ; bi < nbeadtypes ; bi++ ) {
for ( i = 0 ; i < xbins ; i++ ) {
/* All bins are cylinders and therefore constant in yindex */
binvolume = PI*(2*i*xbinwidth + xbinwidth*xbinwidth)*yrange;
for ( j = 0 ; j < ybins ; j++ ) {
density_map[bi].e[ybins*i+j] /= binvolume;
}
}
}
/* if required calculate the theta density profile */
if ( thetabins > 0 ) {
/* Convert the center to an output of the density center */
xav = xav/(double)(beadcount);
yav = yav/(double)(beadcount);
thetabinwidth = 2*PI/(double)(thetabins);
thetaradii = (double*)malloc(thetabins*nbeadtypes*sizeof(double));
thetacounts = (int*)malloc(thetabins*nbeadtypes*sizeof(int));
for ( bi = 0 ; bi < nbeadtypes ; bi++ ) {
for ( t = 0 ; t < thetabins ; t++ ) {
thetaradii[bi*thetabins+t] = 0.0;
thetacounts[bi*thetabins+t] = 0.0;
}
}
/* Maybe there is a nicer way to do this but now I will just repeat the loop over all particles */
for ( pi = 0 ; pi < n_part ; pi++ ) {
for ( bi = 0 ; bi < nbeadtypes ; bi++ ) {
if ( beadids->e[bi] == partCfg[pi].p.type ) {
vecsub(center,partCfg[pi].r.p,pvector);
vector_product(axis,pvector,vectprod);
xdist = sqrt(sqrlen(vectprod)/sqrlen(axis));
ydist = scalar(axis,pvector)/sqrt(sqrlen(axis));
/* Center the coordinates */
xdist = xdist - xav;
ydist = ydist - yav;
rdist = sqrt(xdist*xdist+ydist*ydist);
if ( ydist >= 0 ) {
theta = acos(xdist/rdist);
} else {
theta = 2*PI-acos(xdist/rdist);
}
tindex = (int)(floor(theta/thetabinwidth));
thetaradii[bi*thetabins+tindex] += xdist + xav;
thetacounts[bi*thetabins+tindex] += 1;
if ( tindex >= thetabins ) {
fprintf(stderr,"ERROR: outside density_profile array bounds in calc_radial_density_map"); fflush(NULL); errexit();
} else {
density_profile[bi].e[tindex] += 1;
}
}
}
}
/* normalize the theta densities*/
for ( bi = 0 ; bi < nbeadtypes ; bi++ ) {
for ( t = 0 ; t < thetabins ; t++ ) {
rdist = thetaradii[bi*thetabins+t]/(double)(thetacounts[bi*thetabins+t]);
density_profile[bi].e[t] /= rdist*rdist;
}
}
free(thetaradii);
free(thetacounts);
}
// printf("done \n");
return ES_OK;
}
int init_type_array(int type){
if (init_gc() == ES_ERROR)
return ES_ERROR;
updatePartCfg(WITHOUT_BONDS);
if (!partCfg)
return ES_ERROR;
int type_index=-1;
type_index= (Type.max_entry++);
if ( type_index == number_of_type_lists ) {
reallocate_global_type_list(number_of_type_lists*2);
}
Type.index = (int *) realloc ( (void *) Type.index, sizeof(int)*Type.max_entry);
//reallocate the array that holds the particle type and points to the type index used for the type_list
if ( type >= Index.max_entry ) {
Index.type= (int * ) realloc( (void *) Index.type, (type+1)*sizeof(int));
Index.max_entry = type + 1;
}
for (int i=0; i<Type.max_entry; i++)
Index.type[i]=-1;
if (Type.index == (int *) 0 || Index.type == (int *) 0)
return ES_ERROR;
//allocates a list for ids for as many entries as there are particles right now
if ( !(partCfg) || type < 0 ) {
return ES_ERROR;
}
Type.index[type_index]=type;
//fill in array type_index_of_type
for (int i=0; i<Type.max_entry; i++ ) {
Index.type[Type.index[i]] = i;
}
int t_c = 0; //index
type_array[Index.type[type]].id_list = (int *) malloc (sizeof (int) * n_part);
for (int i=0; i<n_part; i++) {
if ( partCfg[i].p.type==type )
type_array[Index.type[type]].id_list[t_c++]=partCfg[i].p.identity;
}
int max_size=n_part;
if ( t_c != 0 ) {
while ( t_c < (double) max_size/4.0) {
max_size= floor( (double ) max_size/2.0);
}
// now the array is shrinked to at least 4 times the highest entry
type_array[Index.type[type]].id_list= (int *) realloc( (void *) type_array[Index.type[type]].id_list, sizeof(int)*2*max_size);
type_array[Index.type[type]].max_entry = t_c;
type_array[Index.type[type]].cur_size = max_size*2;
} else {
//no particles of the given type were found, so leave array size fixed at a reasonable start entry 64 ints in this case
type_array[Index.type[type]].id_list= (int *) realloc( (void *) type_array[Index.type[type]].id_list, sizeof(int)*64);
type_array[Index.type[type]].max_entry = t_c;
type_array[Index.type[type]].cur_size = 64;
}
//fill remaining entries with -1
for (int i=type_array[Index.type[type]].max_entry; i<type_array[Index.type[type]].cur_size; i++) {
type_array[Index.type[type]].id_list[i] = -1;
}
Type_array_init = 1;
return ES_OK;
}
void calc_gyration_tensor(int type, double **_gt)
{
int i, j, count;
double com[3];
double eva[3],eve0[3],eve1[3],eve2[3];
double *gt=NULL, tmp;
double Smatrix[9],p1[3];
for (i=0; i<9; i++) Smatrix[i] = 0;
/* 3*ev, rg, b, c, kappa, eve0[3], eve1[3], eve2[3]*/
*_gt = gt = (double*)realloc(gt,16*sizeof(double));
updatePartCfg(WITHOUT_BONDS);
/* Calculate the position of COM */
centermass(type,com);
/* Calculate the gyration tensor Smatrix */
count=0;
for (i=0;i<n_part;i++) {
if ((partCfg[i].p.type == type) || (type == -1)) {
for ( j=0; j<3 ; j++ ) {
p1[j] = partCfg[i].r.p[j] - com[j];
}
count ++;
Smatrix[0] += p1[0]*p1[0];
Smatrix[1] += p1[0]*p1[1];
Smatrix[2] += p1[0]*p1[2];
Smatrix[4] += p1[1]*p1[1];
Smatrix[5] += p1[1]*p1[2];
Smatrix[8] += p1[2]*p1[2];
}
}
/* use symmetry */
Smatrix[3]=Smatrix[1];
Smatrix[6]=Smatrix[2];
Smatrix[7]=Smatrix[5];
for (i=0;i<9;i++){
Smatrix[i] /= count;
}
/* Calculate the eigenvalues of Smatrix */
i=calc_eigenvalues_3x3(Smatrix, eva);
tmp=0.0;
for (i=0;i<3;i++) {
/* Eigenvalues */
gt[i] = eva[i];
tmp += eva[i];
}
i=calc_eigenvector_3x3(Smatrix,eva[0],eve0);
i=calc_eigenvector_3x3(Smatrix,eva[1],eve1);
i=calc_eigenvector_3x3(Smatrix,eva[2],eve2);
gt[3] = tmp; /* Squared Radius of Gyration */
gt[4] = eva[0]-0.5*(eva[1]+eva[2]); /* Asphericity */
gt[5] = eva[1]-eva[2]; /* Acylindricity */
gt[6] = (gt[4]*gt[4]+0.75*gt[5]*gt[5])/(gt[3]*gt[3]); /* Relative shape anisotropy */
/* Eigenvectors */
for (j=0;j<3;j++) {
gt[7+j]=eve0[j];
gt[10+j]=eve1[j];
gt[13+j]=eve2[j];
}
}
/**
This routine calculates the orientational order parameter for a
lipid bilayer.
*/
int orient_order(double* result, double* stored_dirs)
{
double dir[3];
double refdir[3] = {0,0,1};
double sumdir[3] = {0,0,0};
double zref;
int bilayer_cnt;
int i,atom,tmpzdir;
double dp;
double len;
IntList l_orient;
init_intlist(&l_orient);
realloc_intlist(&l_orient, n_molecules);
bilayer_cnt = 0;
*result = 0;
// Check to see if the grid has been set and if not then interpret
if ( xdir + ydir + zdir == -3 ) {
tmpzdir = 2;
} else {
tmpzdir = zdir;
};
/* Update particles */
updatePartCfg(WITHOUT_BONDS);
/* Make sure particles are sorted */
if (!sortPartCfg()) {
char *errtxt = runtime_error(128);
ERROR_SPRINTF(errtxt, "{035 could not sort partCfg, particles have to start at 0 and have consecutive identities} ");
return ES_ERROR;
}
/* Calculate the reference z position as its mean.*/
zref = calc_zref( tmpzdir );
/* Calculate the orientation of all the lipids in turn and include
only UP or DOWN lipids in a calculation of the overall orientation
direction of the bilayer .. ie the reference vector from which we
can calculate the orientational order. */
for ( i = 0 ; i < n_molecules ; i++) {
atom = topology[i].part.e[0];
l_orient.e[i] = lipid_orientation(atom,partCfg,zref,dir,refdir);
stored_dirs[i*3] = dir[0];
stored_dirs[i*3+1] = dir[1];
stored_dirs[i*3+2] = dir[2];
if ( l_orient.e[i] == LIPID_UP ) {
sumdir[0] += dir[0];
sumdir[1] += dir[1];
sumdir[2] += dir[2];
bilayer_cnt++;
}
if ( l_orient.e[i] == LIPID_DOWN ) {
sumdir[0] -= dir[0];
sumdir[1] -= dir[1];
sumdir[2] -= dir[2];
bilayer_cnt++;
}
}
/* Normalise the bilayer normal vector */
len = 0.0;
for ( i = 0 ; i < 3 ; i++) {
sumdir[i] = sumdir[i]/(double)(bilayer_cnt);
len += sumdir[i]*sumdir[i];
}
for ( i = 0 ; i < 3 ; i++) {
sumdir[i] = sumdir[i]/sqrt(len);
}
/* Calculate the orientational order */
for ( i = 0 ; i < n_molecules ; i++ ) {
dir[0] = stored_dirs[i*3];
dir[1] = stored_dirs[i*3+1];
dir[2] = stored_dirs[i*3+2];
if ( l_orient.e[i] != LIPID_STRAY && l_orient.e[i] != REAL_LIPID_STRAY ) {
dp = scalar(dir,sumdir);
*result += dp*dp*1.5-0.5;
}
}
realloc_intlist(&l_orient, 0);
*result = *result/(double)(bilayer_cnt);
return ES_OK;
}
/** This routine performs must of the work involved in the analyze
modes2d command. A breakdown of what the routine does is as
follows
\li fftw plans and in / out arrays are initialized as required
\li calculate height function is called
\li The height function is fourier transformed using the fftw library.
Note: argument switch_fluc
switch_fluc == 1 for height grid
switch_fluc == 0 for thickness
*/
int modes2d(fftw_complex* modes, int switch_fluc) {
/* All these variables need to be static so that the fftw3 plan can
be initialised and reused */
static fftw_plan mode_analysis_plan; // height grid
/** Input values for the fft */
static double* height_grid;
/** Output values for the fft */
static fftw_complex* result;
/**
Every time a change is made to the grid calculate the fftw plan
for the subsequent fft and destroy any existing plans
*/
if ( mode_grid_changed ) {
STAT_TRACE(fprintf(stderr,"%d,initializing fftw for mode analysis \n",this_node));
if ( xdir + ydir + zdir == -3 ) {
char *errtxt = runtime_error(128);
ERROR_SPRINTF(errtxt,"{092 attempt to perform mode analysis with uninitialized grid} ");
return -1;
}
STAT_TRACE(fprintf(stderr,"%d,destroying old fftw plan \n",this_node));
/* Make sure all memory is free and old plan is destroyed. It's ok
to call these functions on uninitialised pointers I think */
fftw_free(result);
fftw_free(height_grid);
fftw_destroy_plan(mode_analysis_plan);
fftw_cleanup();
/* Allocate memory for input and output arrays */
height_grid = (double*) malloc((mode_grid_3d[xdir])*sizeof(double)*mode_grid_3d[ydir]);
result = (fftw_complex*) malloc((mode_grid_3d[ydir]/2+1)*(mode_grid_3d[xdir])*sizeof(fftw_complex));
mode_analysis_plan = fftw_plan_dft_r2c_2d(mode_grid_3d[xdir],mode_grid_3d[ydir],height_grid, result,FFTW_ESTIMATE);
STAT_TRACE(fprintf(stderr,"%d,created new fftw plan \n",this_node));
mode_grid_changed = 0;
}
/* Update particles */
updatePartCfg(WITHOUT_BONDS);
//Make sure particles are sorted
if (!sortPartCfg()) {
fprintf(stderr,"%d,could not sort partCfg \n",this_node);
return -1;
}
if ( !calc_fluctuations(height_grid, switch_fluc)) {
char *errtxt = runtime_error(128);
ERROR_SPRINTF(errtxt,"{034 calculation of height grid failed } ");
return -1;
}
STAT_TRACE(fprintf(stderr,"%d,calling fftw \n",this_node));
fftw_execute(mode_analysis_plan);
/* Copy result to modes */
memcpy(modes, result, mode_grid_3d[xdir]*(mode_grid_3d[ydir]/2 + 1)*sizeof(fftw_complex));
STAT_TRACE(fprintf(stderr,"%d,called fftw \n",this_node));
return 1;
}
/** This routine calculates density profiles for given bead types as a
function of height relative to the bilayer midplane where the
bilayer is assumed to wrap around a sphere of radius r and center
cx,cy,cz.
\li The radius value of each bead is then calculated relative to
the colloid radius and the population of the relevant bin
is increased.
**/
int bilayer_density_profile_sphere (IntList *beadids, double rrange , DoubleList *density_profile, double radius, double center[3]) {
int i,j;
int thisbin,nbins;
double binwidth;
int nbeadtypes,l_orient;
double relativeradius;
double rvec[3];
double direction[3];
double innerr;
double outerr;
double binvolume;
double piconst;
double rs;
nbins = density_profile[0].max;
nbeadtypes=beadids->max;
binwidth = 2*rrange/(double)nbins;
/* Update particles */
updatePartCfg(WITHOUT_BONDS);
//Make sure particles are sorted
if (!sortPartCfg()) {
char *errtxt = runtime_error(128);
ERROR_SPRINTF(errtxt,"{094 could not sort partCfg} ");
return -1;
}
if ( density_profile == NULL ) {
char *errtxt = runtime_error(128);
ERROR_SPRINTF(errtxt,"{095 density_profile not initialized in calc_bilayer_density_profile } ");
return -1;
}
// Do this to fold the particles
fold_all( );
for (i = 0 ; i < n_total_particles ; i++) {
for ( j = 0 ; j < nbeadtypes ; j++ ) {
if ( beadids->e[j] == partCfg[i].p.type ) {
/* What is the relative height compared to the grid */
get_mi_vector(rvec,partCfg[i].r.p,center);
relativeradius = sqrt(sqrlen(rvec)) - radius;
/* If the particle is within our zrange then add it to the profile */
if ( ( -rrange < relativeradius) && ( relativeradius < rrange) ) {
thisbin = (int)(floor((relativeradius+rrange)/binwidth));
if ( thisbin < 0 || thisbin >= density_profile[j].max ) {
char *errtxt = runtime_error(128);
ERROR_SPRINTF(errtxt,"{095 bin is outside range } ");
return -1;
}
l_orient = lipid_orientation(i,partCfg,0.0,direction,rvec);
/* Distinguish between lipids that are in the top and bottom layers */
if ( l_orient == LIPID_UP ) {
density_profile[j].e[thisbin] += 1.0;
}
if ( l_orient == LIPID_DOWN ) {
density_profile[2*nbeadtypes-j-1].e[thisbin] += 1.0;
}
}
}
}
}
/* Normalize the density profile */
piconst = (4.0*3.141592)/(3.0);
rs = radius - rrange;
for ( i = 0 ; i < 2*nbeadtypes ; i++ ) {
for ( j = 0 ; j < nbins ; j++ ) {
innerr = j*binwidth+rs;
outerr = (j+1)*binwidth + rs;
binvolume = piconst*(outerr*outerr*outerr - innerr*innerr*innerr);
density_profile[i].e[j] = density_profile[i].e[j]/binvolume;
}
}
return 1;
}
/* parser for hole cluster analyzation:
analyze holes <prob_part_type_number> <mesh_size>.
Needs feature LENNARD_JONES compiled in. */
int tclcommand_analyze_parse_holes(Tcl_Interp *interp, int argc, char **argv)
{
int i,j;
int probe_part_type;
int mesh_size=1, meshdim[3];
double freevol=0.0;
char buffer[TCL_INTEGER_SPACE+TCL_DOUBLE_SPACE];
IntList mesh;
int n_holes;
int **holes;
int max_size=0;
int *surface;
#ifndef LENNARD_JONES
Tcl_AppendResult(interp, "analyze holes needs feature LENNARD_JONES compiled in.\n", (char *)NULL);
return TCL_ERROR;
#endif
/* check # of parameters */
if (argc < 2) {
Tcl_AppendResult(interp, "analyze holes needs 2 parameters:\n", (char *)NULL);
Tcl_AppendResult(interp, "<prob_part_type_number> <mesh_size>", (char *)NULL);
return TCL_ERROR;
}
/* check parameter types */
if( (! ARG_IS_I(0, probe_part_type)) ||
(! ARG_IS_I(1, mesh_size)) ) {
Tcl_AppendResult(interp, "analyze holes needs 2 parameters of type and meaning:\n", (char *)NULL);
Tcl_AppendResult(interp, "INT INT\n", (char *)NULL);
Tcl_AppendResult(interp, "<prob_part_type_number> <mesh_size>", (char *)NULL);
return TCL_ERROR;
}
/* check parameter values */
if( probe_part_type > n_particle_types || probe_part_type < 0 ) {
Tcl_AppendResult(interp, "analyze holes: probe particle type number does not exist", (char *)NULL);
return TCL_ERROR;
}
if( mesh_size < 1 ) {
Tcl_AppendResult(interp, "analyze holes: mesh size must be positive (min=1)", (char *)NULL);
return TCL_ERROR;
}
/* preparation */
updatePartCfg(WITHOUT_BONDS);
meshdim[0]=mesh_size;
meshdim[1]=mesh_size;
meshdim[2]=mesh_size;
alloc_intlist(&mesh, (meshdim[0]*meshdim[1]*meshdim[2]));
/* perform free space identification*/
create_free_volume_grid(mesh, meshdim, probe_part_type);
/* perfrom hole cluster algorithm */
n_holes = cluster_free_volume_grid(mesh, meshdim, &holes);
/* surface to volume ratio */
surface = (int *) malloc(sizeof(int)*(n_holes+1));
cluster_free_volume_surface(mesh, meshdim, n_holes, holes, surface);
/* calculate accessible volume / max size*/
for ( i=0; i<=n_holes; i++ ) {
freevol += holes[i][0];
if ( holes[i][0]> max_size ) max_size = holes[i][0];
}
/* Append result to tcl interpreter */
Tcl_AppendResult(interp, "{ n_holes mean_hole_size max_hole_size free_volume_fraction { sizes } { surfaces } { element_lists } } ", (char *)NULL);
Tcl_AppendResult(interp, "{", (char *)NULL);
/* number of holes */
sprintf(buffer,"%d ",n_holes+1); Tcl_AppendResult(interp, buffer, " ", (char *)NULL);
/* mean hole size */
sprintf(buffer,"%f ",freevol/(n_holes+1.0)); Tcl_AppendResult(interp, buffer, " ", (char *)NULL);
/* max hole size */
sprintf(buffer,"%d ",max_size); Tcl_AppendResult(interp, buffer, " ", (char *)NULL);
/* free volume fraction */
sprintf(buffer,"%f ",freevol/(meshdim[0]*meshdim[1]*meshdim[2]));
Tcl_AppendResult(interp, buffer, " ", (char *)NULL);
/* hole sizes */
Tcl_AppendResult(interp, "{ ", (char *)NULL);
for ( i=0; i<=n_holes; i++ ) {
sprintf(buffer,"%d ",holes[i][0]); Tcl_AppendResult(interp, buffer, " ", (char *)NULL);
}
Tcl_AppendResult(interp, "} ", (char *)NULL);
/* hole surfaces */
Tcl_AppendResult(interp, "{ ", (char *)NULL);
for ( i=0; i<=n_holes; i++ ) {
sprintf(buffer,"%d ",surface[i]); Tcl_AppendResult(interp, buffer, " ", (char *)NULL);
}
Tcl_AppendResult(interp, "} ", (char *)NULL);
/* hole elements */
Tcl_AppendResult(interp, "{ ", (char *)NULL);
for ( i=0; i<=n_holes; i++ ) {
Tcl_AppendResult(interp, "{ ", (char *)NULL);
for ( j=1; j <= holes[i][0]; j++ ) {
sprintf(buffer,"%d",holes[i][j]);
Tcl_AppendResult(interp, buffer, " ",(char *)NULL);
}
Tcl_AppendResult(interp, "} ", (char *)NULL);
}
Tcl_AppendResult(interp, "} ", (char *)NULL);
Tcl_AppendResult(interp, "}", (char *)NULL);
/* free allocated memory */
realloc_intlist(&mesh, 0);
free(surface);
for ( i=0; i<=n_holes; i++ ) { free(holes[i]); }
free(holes);
return (TCL_OK);
}
int tclcommand_imd_parse_pos(Tcl_Interp *interp, int argc, char **argv)
{
enum flag {NONE, UNFOLDED, FOLD_CHAINS};
double shift[3] = {0.0,0.0,0.0};
//double part_selected=n_total_particles;
float *coord;
int flag = NONE;
int i, j;
// Determine how many arguments we have and set the value of flag
switch (argc)
{
case 2:
flag = NONE;
break;
case 3:
{
if (ARG_IS_S(2,"-unfolded"))
{flag = UNFOLDED;}
else if (ARG_IS_S(2,"-fold_chains"))
{flag = FOLD_CHAINS;}
else{
Tcl_AppendResult(interp, "wrong flag to",argv[0],
" positions: should be \" -fold_chains or -unfolded \"",
(char *) NULL);
return (TCL_ERROR);
}
}
break;
default:
Tcl_AppendResult(interp, "wrong # args: should be \"",
argv[0], " positions [-flag]\"",
(char *) NULL);
return (TCL_ERROR);
}
if (!initsock) {
Tcl_AppendResult(interp, "no connection",
(char *) NULL);
return (TCL_OK);
}
if (!sock) {
if (tclcommand_imd_print_check_connect(interp) == TCL_ERROR)
return (TCL_ERROR);
/* no VMD is ok, but tell the user */
if (!sock) {
Tcl_AppendResult(interp, "no connection",
(char *) NULL);
return (TCL_OK);
}
}
if (tclcommand_imd_print_drain_socket(interp) == TCL_ERROR)
return (TCL_ERROR);
/* we do not consider a non connected VMD as error, but tell the user */
if (!sock) {
Tcl_AppendResult(interp, "no connection",
(char *) NULL);
return (TCL_OK);
}
if (!(vmdsock_selwrite(sock, 60) > 0)) {
Tcl_AppendResult(interp, "could not write to IMD socket.",
(char *) NULL);
return (TCL_ERROR);
}
if (n_part != max_seen_particle + 1) {
Tcl_AppendResult(interp, "for IMD, store particles consecutively starting with 0.",
(char *) NULL);
return (TCL_ERROR);
}
updatePartCfg(WITH_BONDS);
coord = (float*)Utils::malloc(n_part*3*sizeof(float));
/* sort partcles according to identities */
for (i = 0; i < n_part; i++) {
int dummy[3] = {0,0,0};
double tmpCoord[3];
tmpCoord[0] = partCfg[i].r.p[0];
tmpCoord[1] = partCfg[i].r.p[1];
tmpCoord[2] = partCfg[i].r.p[2];
if (flag == NONE) { // perform folding by particle
fold_position(tmpCoord, dummy);
}
j = 3*partCfg[i].p.identity;
coord[j ] = tmpCoord[0];
coord[j + 1] = tmpCoord[1];
coord[j + 2] = tmpCoord[2];
}
// Use information from the analyse set command to fold chain molecules
if ( flag == FOLD_CHAINS ){
if(analyze_fold_molecules(coord, shift ) != TCL_OK){
Tcl_AppendResult(interp, "could not fold chains: \"analyze set chains <chain_start> <n_chains> <chain_length>\" must be used first",
(char *) NULL);
return (TCL_ERROR);
}
}
if (imd_send_fcoords(sock, n_part, coord)) {
Tcl_AppendResult(interp, "could not write to IMD socket.",
(char *) NULL);
return (TCL_ERROR);
}
free(coord);
Tcl_AppendResult(interp, "connected",
(char *) NULL);
return (TCL_OK);
}
int calc_fluctuations ( double* height_grid, int switch_fluc ) {
if (switch_fluc == 1){
STAT_TRACE(fprintf(stderr,"%d,calculating height grid \n",this_node));
} else { if (switch_fluc == 0) {
STAT_TRACE(fprintf(stderr,"%d,calculating thickness \n",this_node));
} else {
char *errtxt = runtime_error(128);
ERROR_SPRINTF(errtxt,"{097 Wrong argument in calc_fluctuations function} ");
return -1;
}
}
int i, j, gi, gj;
double grid_size[2];
double direction[3];
double refdir[3] = {0,0,1};
double* height_grid_up;
double* height_grid_down;
int* grid_parts;
int* grid_parts_up;
int* grid_parts_down;
double zreflocal, zref;
int nup;
int ndown;
int nstray;
int nrealstray;
int l_orient;
double norm;
int xi, yi;
double meanval;
int nonzerocnt, gapcnt;
if ( xdir + ydir + zdir == -3 ) {
char *errtxt = runtime_error(128);
ERROR_SPRINTF(errtxt,"{092 attempt to calculate height grid / thickness with uninitialized grid} ");
return -1;
}
if ( height_grid == NULL ) {
char *errtxt = runtime_error(128);
ERROR_SPRINTF(errtxt,"{093 you must allocate memory for the height grid / thickness first} ");
return -1;
}
/* Allocate memory for height grid / thickness arrays and initialize these arrays */
height_grid_up = (double*) malloc((mode_grid_3d[xdir])*sizeof(double)*mode_grid_3d[ydir]);
height_grid_down = (double*) malloc((mode_grid_3d[xdir])*sizeof(double)*mode_grid_3d[ydir]);
grid_parts_up = (int*) malloc((mode_grid_3d[xdir])*sizeof(int)*mode_grid_3d[ydir]);
grid_parts_down = (int*) malloc((mode_grid_3d[xdir])*sizeof(int)*mode_grid_3d[ydir]);
grid_parts = (int*) malloc((mode_grid_3d[xdir])*sizeof(int)*mode_grid_3d[ydir]);
for ( i = 0 ; i < mode_grid_3d[xdir] ; i++) {
for ( j = 0 ; j < mode_grid_3d[ydir] ; j++) {
height_grid[j+i*mode_grid_3d[xdir]] = 0;
grid_parts[j+i*mode_grid_3d[xdir]] = 0;
height_grid_up[j+i*mode_grid_3d[xdir]] = 0;
grid_parts_up[j+i*mode_grid_3d[xdir]] = 0;
height_grid_down[j+i*mode_grid_3d[xdir]] = 0;
grid_parts_down[j+i*mode_grid_3d[xdir]] = 0;
}
}
/* Calculate physical size of grid mesh */
grid_size[xdir] = box_l[xdir]/(double)mode_grid_3d[xdir];
grid_size[ydir] = box_l[ydir]/(double)mode_grid_3d[ydir];
/* Update particles */
updatePartCfg(WITHOUT_BONDS);
//Make sure particles are sorted
if (!sortPartCfg()) {
char *errtxt = runtime_error(128);
ERROR_SPRINTF(errtxt,"{094 could not sort partCfg} ");
return -1;
}
/* Find the mean z position of folded coordinates*/
zref = calc_zref( zdir );
/* Calculate an initial height function of all particles */
for (i = 0 ; i < n_total_particles ; i++) {
gi = floor( partCfg[i].r.p[xdir]/grid_size[xdir] );
gj = floor( partCfg[i].r.p[ydir]/grid_size[ydir] );
height_grid[gj + gi*mode_grid_3d[xdir]] += partCfg[i].r.p[zdir];
grid_parts[gj + gi*mode_grid_3d[xdir]] += 1;
}
/* Normalise the initial height function */
for ( i = 0 ; i < mode_grid_3d[xdir] ; i++) {
for ( j = 0 ; j < mode_grid_3d[ydir] ; j++) {
if ( grid_parts[j+i*mode_grid_3d[xdir]] > 0 ) {
height_grid[j+i*mode_grid_3d[xdir]] = height_grid[j+i*mode_grid_3d[xdir]]/(double)(grid_parts[j+i*mode_grid_3d[xdir]]);
} else {
height_grid[j+i*mode_grid_3d[xdir]] = zref;
}
}
}
/* We now use this initial height function to calculate the
lipid_orientation and thereby calculate populations in upper and
lower leaflets */
/* Calculate the non normalized height function based on all lipids */
nup = ndown = nstray = nrealstray = 0;
for (i = 0 ; i < n_total_particles ; i++) {
gi = floor( partCfg[i].r.p[xdir]/grid_size[xdir] );
gj = floor( partCfg[i].r.p[ydir]/grid_size[ydir] );
zreflocal = height_grid[gj+gi*mode_grid_3d[xdir]];
l_orient = lipid_orientation(i,partCfg,zreflocal,direction,refdir);
if ( l_orient != LIPID_STRAY && l_orient != REAL_LIPID_STRAY) {
if ( l_orient == LIPID_UP ) {
nup++;
height_grid_up[gj + gi*mode_grid_3d[xdir]] += partCfg[i].r.p[zdir] - zref;
grid_parts_up[gj + gi*mode_grid_3d[xdir]] += 1;
} else if ( l_orient == LIPID_DOWN ) {
ndown++;
height_grid_down[gj + gi*mode_grid_3d[xdir]] += partCfg[i].r.p[zdir] - zref;
grid_parts_down[gj + gi*mode_grid_3d[xdir]] += 1;
}
} else {
if ( l_orient == REAL_LIPID_STRAY ) {
nrealstray++;
}
}
}
/*
if ( nrealstray > 0 || nstray > 0) {
printf("Warning: there were %d stray lipid particles in height calculation \n", nrealstray);
}
printf(" Lipid particles up = %d , Lipid particles down = %d \n",nup, ndown); */
STAT_TRACE(fprintf(stderr,"%d, Lipids up = %d , Lipids down = %d \n",this_node, nup, ndown));
/* Reinitialise the height grid */
for ( i = 0 ; i < mode_grid_3d[xdir] ; i++) {
for ( j = 0 ; j < mode_grid_3d[ydir] ; j++) {
height_grid[j+i*mode_grid_3d[xdir]] = 0.0;
grid_parts[j+i*mode_grid_3d[xdir]] = 0;
}
}
/* Norm we normalize the height function according the number of
points in each grid cell */
norm = 1.0;
for ( i = 0 ; i < mode_grid_3d[xdir] ; i++) {
for ( j = 0 ; j < mode_grid_3d[ydir] ; j++) {
if ( ( grid_parts_up[j + i*mode_grid_3d[xdir]] > 0 ) && ( grid_parts_down[j + i*mode_grid_3d[xdir]] > 0 ) ) {
/*
This is where we distinguish between height_grid and thickness:
h = .5*(h_up + h_down)
t = h_up - h_down
*/
if (switch_fluc == 1)
height_grid[j+i*mode_grid_3d[xdir]] =
0.5*norm*((height_grid_up[j+i*mode_grid_3d[xdir]])/(double)(grid_parts_up[j + i*mode_grid_3d[xdir]]) +
(height_grid_down[j+i*mode_grid_3d[xdir]])/(double)(grid_parts_down[j + i*mode_grid_3d[xdir]]));
else
height_grid[j+i*mode_grid_3d[xdir]] =
norm*((height_grid_up[j+i*mode_grid_3d[xdir]])/(double)(grid_parts_up[j + i*mode_grid_3d[xdir]]) -
(height_grid_down[j+i*mode_grid_3d[xdir]])/(double)(grid_parts_down[j + i*mode_grid_3d[xdir]]));
grid_parts[j+i*mode_grid_3d[xdir]] = grid_parts_up[j + i*mode_grid_3d[xdir]] + grid_parts_down[j + i*mode_grid_3d[xdir]];
} else {
// Either upper or lower layer has no lipids
height_grid[j+i*mode_grid_3d[xdir]] = 0.0;
grid_parts[j+i*mode_grid_3d[xdir]] = 0;
}
}
}
/* Check height grid for zero values and substitute mean of surrounding cells */
gapcnt = 0;
for ( i = 0 ; i < mode_grid_3d[xdir] ; i++) {
for ( j = 0 ; j < mode_grid_3d[ydir] ; j++) {
if ( grid_parts[j + i*mode_grid_3d[xdir]] == 0) {
meanval = 0.0;
nonzerocnt = 0;
for ( xi = (i-1) ; xi <= (i+1) ; xi++) {
for ( yi = (j-1) ; yi <= (j+1) ; yi++) {
if ( height_grid[yi+xi*mode_grid_3d[xdir]] != 0 ) {
meanval += height_grid[yi+xi*mode_grid_3d[xdir]];
nonzerocnt++;
}
}
}
if ( nonzerocnt == 0 ) {
char *errtxt = runtime_error(128);
ERROR_SPRINTF(errtxt,"{095 hole in membrane} ");
return -1;
}
gapcnt++;
}
}
}
if ( gapcnt != 0 ) {
fprintf(stderr,"Warning: %d, gridpoints with no particles \n",gapcnt);
fflush(stdout);
}
free(grid_parts);
free(height_grid_up);
free(height_grid_down);
free(grid_parts_up);
free(grid_parts_down);
return 1;
}
int calc_cylindrical_average(std::vector<double> center, std::vector<double> direction, double length,
double radius, int bins_axial, int bins_radial, std::vector<int> types,
std::map<std::string, std::vector<std::vector<std::vector<double> > > > &distribution)
{
int index_axial;
int index_radial;
double binwd_axial = length / bins_axial;
double binwd_radial = radius / bins_radial;
// Select all particle types if the only entry in types is -1
bool all_types = false;
if (types.size() == 1 && types[0] == -1) all_types = true;
distribution.insert( std::pair<std::string, std::vector<std::vector<std::vector<double> > > >
("density", std::vector<std::vector<std::vector<double> > >(types.size())) );
distribution.insert( std::pair<std::string, std::vector<std::vector<std::vector<double> > > >
("v_r", std::vector<std::vector<std::vector<double> > >(types.size())) );
distribution.insert( std::pair<std::string, std::vector<std::vector<std::vector<double> > > >
("v_t", std::vector<std::vector<std::vector<double> > >(types.size())) );
for (unsigned int type = 0; type < types.size(); type++) {
distribution["density"][type].resize(bins_radial);
distribution["v_r"][type].resize(bins_radial);
distribution["v_t"][type].resize(bins_radial);
for (int index_radial = 0; index_radial < bins_radial; index_radial++) {
distribution["density"][type][index_radial].assign(bins_axial, 0.0);
distribution["v_r"][type][index_radial].assign(bins_axial, 0.0);
distribution["v_t"][type][index_radial].assign(bins_axial, 0.0);
}
}
// Update particles
updatePartCfg(WITHOUT_BONDS);
// Make sure particles are folded
for (int i = 0 ; i < n_part ; i++) {
fold_coordinate(partCfg[i].r.p,partCfg[i].m.v,partCfg[i].l.i,0);
fold_coordinate(partCfg[i].r.p,partCfg[i].m.v,partCfg[i].l.i,1);
fold_coordinate(partCfg[i].r.p,partCfg[i].m.v,partCfg[i].l.i,2);
}
// Declare variables for the density calculation
double height, dist, v_radial, v_axial;
double norm_direction = utils::veclen(direction);
std::vector<double> pos(3), vel(3), diff, hat;
for (int part_id = 0; part_id < n_part; part_id++) {
for (unsigned int type_id = 0; type_id < types.size(); type_id++) {
if ( types[type_id] == partCfg[part_id].p.type || all_types) {
pos[0] = partCfg[part_id].r.p[0];
pos[1] = partCfg[part_id].r.p[1];
pos[2] = partCfg[part_id].r.p[2];
vel[0] = partCfg[part_id].m.v[0];
vel[1] = partCfg[part_id].m.v[1];
vel[2] = partCfg[part_id].m.v[2];
// Find the vector from center to the current particle
diff = utils::vecsub(pos,center);
// Find the height of the particle above the axis (height) and
// the distance from the center point (dist)
hat = utils::cross_product(direction,diff);
height = utils::veclen(hat);
dist = utils::dot_product(direction,diff) / norm_direction;
// Determine the components of the velocity parallel and
// perpendicular to the direction vector
if ( height == 0 )
v_radial = utils::veclen(utils::cross_product(vel,direction)) / norm_direction;
else
v_radial = utils::dot_product(vel,hat) / height;
v_axial = utils::dot_product(vel,direction) / norm_direction;
// Work out relevant indices for x and y
index_radial = static_cast<int>( floor(height / binwd_radial) );
index_axial = static_cast<int>( floor((dist + 0.5*length) / binwd_axial) );
if ( (index_radial < bins_radial && index_radial >= 0) &&
(index_axial < bins_axial && index_axial >= 0) ) {
distribution["density"][type_id][index_radial][index_axial] += 1;
distribution["v_r"][type_id][index_radial][index_axial] += v_radial;
distribution["v_t"][type_id][index_radial][index_axial] += v_axial;
}
}
}
}
// Now we turn the counts into densities by dividing by one radial
// bin (binvolume). We also divide the velocites by the counts.
double binvolume;
for (unsigned int type_id = 0; type_id < types.size(); type_id++) {
for (int index_radial = 0 ; index_radial < bins_radial ; index_radial++) {
// All bins are cylindrical shells of thickness binwd_radial.
// The volume is thus: binvolume = pi*(r_outer - r_inner)^2 * length
if ( index_radial == 0 )
binvolume = M_PI * binwd_radial*binwd_radial * length;
else
binvolume = M_PI * (index_radial*index_radial + 2*index_radial) * binwd_radial*binwd_radial * length;
for (int index_axial = 0 ; index_axial < bins_axial ; index_axial++) {
if ( distribution["density"][type_id][index_radial][index_axial] != 0 ) {
distribution["v_r"][type_id][index_radial][index_axial] /= distribution["density"][type_id][index_radial][index_axial];
distribution["v_t"][type_id][index_radial][index_axial] /= distribution["density"][type_id][index_radial][index_axial];
distribution["density"][type_id][index_radial][index_axial] /= binvolume;
}
}
}
}
return ES_OK;
}
int tclcommand_analyze_parse_and_print_dipmom_mol(Tcl_Interp *interp,int argc, char **argv)
{
#ifndef ELECTROSTATICS
Tcl_ResetResult(interp);
Tcl_AppendResult(interp, "calc_dipole_mol is not possible without ELECTROSTATICS", (char *)NULL);
return (TCL_ERROR);
#else
int k,type;
char buffer[TCL_DOUBLE_SPACE];
double dipole[4];
updatePartCfg(WITHOUT_BONDS);
if (!sortPartCfg()) {
char *errtxt = runtime_error(128);
ERROR_SPRINTF(errtxt, "{059 parse_and_print_dipole: could not sort particle config, particle ids not consecutive?} ");
return TCL_ERROR;
}
if (n_molecules==0) {
Tcl_ResetResult(interp);
Tcl_AppendResult(interp, "No molecules defined !", (char *)NULL);
return (TCL_ERROR);
}
if (argc < 2) {
Tcl_ResetResult(interp);
Tcl_AppendResult(interp, "usage: analyze parse_and_print_dipole_mol <type>", (char *)NULL);
return (TCL_ERROR);
}
if (!ARG1_IS_I(type)) {
Tcl_ResetResult(interp);
Tcl_AppendResult(interp, "usage: analyze parse_and_print_dipole_mol <type>", (char *)NULL);
return (TCL_ERROR);
}
if (ARG0_IS_S("total")){
calc_total_dipolmoment_mol(type,dipole);
sprintf(buffer,"%i ",type);
Tcl_AppendResult(interp,"{ dipolemoment_mol total ",buffer,(char *)NULL);
for (k=0;k<3;k++)
{
sprintf(buffer,"%e ",dipole[k]);
Tcl_AppendResult(interp, buffer,(char *)NULL);
}
sprintf(buffer,"%e",dipole[3]);
Tcl_AppendResult(interp,buffer,"}",(char *)NULL);
}
else if (ARG0_IS_S("absolute")){
calc_absolute_dipolmoment_mol(type,dipole);
sprintf(buffer,"%i ",type);
Tcl_AppendResult(interp,"{ dipolemoment_mol absolute ",buffer,(char *)NULL);
sprintf(buffer,"%e ",dipole[0]);
Tcl_AppendResult(interp, buffer,(char *)NULL);
sprintf(buffer,"%e",dipole[1]);
Tcl_AppendResult(interp,buffer,"}",(char *)NULL);
}
else
{
Tcl_ResetResult(interp);
Tcl_AppendResult(interp, "Feature not implemented", (char *)NULL);
return (TCL_ERROR);
}
argc-=2; argv+=2;
return TCL_OK;
#endif
}