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statistics_chain.c
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statistics_chain.c
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// This file is part of the ESPResSo distribution (http://www.espresso.mpg.de).
// It is therefore subject to the ESPResSo license agreement which you accepted upon receiving the distribution
// and by which you are legally bound while utilizing this file in any form or way.
// There is NO WARRANTY, not even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
// You should have received a copy of that license along with this program;
// if not, refer to http://www.espresso.mpg.de/license.html where its current version can be found, or
// write to Max-Planck-Institute for Polymer Research, Theory Group, PO Box 3148, 55021 Mainz, Germany.
// Copyright (c) 2002-2006; all rights reserved unless otherwise stated.
/** \file statistics_chain.c
Implementation of \ref statistics_chain.h "statistics_chain.h".
*/
#include "statistics.h"
#include "utils.h"
#include "parser.h"
#include "topology.h"
#include "communication.h"
#include "cells.h"
/** Particles' initial positions (needed for g1(t), g2(t), g3(t) in \ref #analyze) */
/*@{*/
float *partCoord_g=NULL, *partCM_g=NULL;
int n_part_g = 0, n_chains_g = 0;
/*@}*/
/** data for a system consisting of chains. TBRS. */
/*@{*/
int chain_start = 0;
int chain_n_chains = 0;
int chain_length = 0;
/*@}*/
void calc_re(double **_re)
{
int i;
double dx,dy,dz;
double dist=0.0,dist2=0.0,dist4=0.0;
double *re=NULL, tmp;
*_re = re = realloc(re,4*sizeof(double));
for (i=0; i<chain_n_chains; i++) {
dx = partCfg[chain_start+i*chain_length + chain_length-1].r.p[0]
- partCfg[chain_start+i*chain_length].r.p[0];
dy = partCfg[chain_start+i*chain_length + chain_length-1].r.p[1]
- partCfg[chain_start+i*chain_length].r.p[1];
dz = partCfg[chain_start+i*chain_length + chain_length-1].r.p[2]
- partCfg[chain_start+i*chain_length].r.p[2];
tmp = (SQR(dx) + SQR(dy) + SQR(dz));
dist += sqrt(tmp);
dist2 += tmp;
dist4 += tmp*tmp;
}
tmp = (double)chain_n_chains;
re[0] = dist/tmp;
re[2] = dist2/tmp;
re[1] = sqrt(re[2] - re[0]*re[0]);
re[3] = sqrt(dist4/tmp - re[2]*re[2]);
}
void calc_re_av(double **_re)
{
int i,j;
double dx,dy,dz;
double dist=0.0,dist2=0.0,dist4=0.0;
double *re=NULL, tmp;
*_re = re = realloc(re,4*sizeof(double));
for (j=0; j<n_configs; j++) {
for (i=0; i<chain_n_chains; i++) {
dx = configs[j][3*(chain_start+i*chain_length + chain_length-1)]
- configs[j][3*(chain_start+i*chain_length)];
dy = configs[j][3*(chain_start+i*chain_length + chain_length-1) + 1]
- configs[j][3*(chain_start+i*chain_length) + 1];
dz = configs[j][3*(chain_start+i*chain_length + chain_length-1) + 2]
- configs[j][3*(chain_start+i*chain_length) + 2];
tmp = (SQR(dx) + SQR(dy) + SQR(dz));
dist += sqrt(tmp);
dist2 += tmp;
dist4 += tmp*tmp;
}
}
tmp = (double)chain_n_chains*n_configs;
re[0] = dist/tmp;
re[2] = dist2/tmp;
re[1] = sqrt(re[2] - re[0]*re[0]);
re[3] = sqrt(dist4/tmp - re[2]*re[2]);
}
void calc_rg(double **_rg)
{
int i, j, p;
double dx,dy,dz, r_CM_x,r_CM_y,r_CM_z;
double r_G=0.0,r_G2=0.0,r_G4=0.0;
double *rg=NULL,IdoubMPC, tmp;
double M;
*_rg = rg = realloc(rg,4*sizeof(double));
for (i=0; i<chain_n_chains; i++) {
M=0.0;
r_CM_x = r_CM_y = r_CM_z = 0.0;
IdoubMPC = 1./(double)chain_length;
for (j=0; j<chain_length; j++) {
p = chain_start+i*chain_length + j;
r_CM_x += partCfg[p].r.p[0]*PMASS(partCfg[p]);
r_CM_y += partCfg[p].r.p[1]*PMASS(partCfg[p]);
r_CM_z += partCfg[p].r.p[2]*PMASS(partCfg[p]);
M += PMASS(partCfg[p]);
}
r_CM_x /= M;
r_CM_y /= M;
r_CM_z /= M;
tmp = 0.0;
for (j=0; j<chain_length; ++j) {
p = chain_start+i*chain_length + j;
dx = partCfg[p].r.p[0] - r_CM_x;
dy = partCfg[p].r.p[1] - r_CM_y;
dz = partCfg[p].r.p[2] - r_CM_z;
tmp += (SQR(dx) + SQR(dy) + SQR(dz));
}
tmp *= IdoubMPC;
r_G += sqrt(tmp);
r_G2 += tmp;
r_G4 += tmp*tmp;
}
tmp = (double)chain_n_chains;
rg[0] = r_G/tmp;
rg[2] = r_G2/tmp;
rg[1] = sqrt(rg[2] - rg[0]*rg[0]);
rg[3] = sqrt(r_G4/tmp - rg[2]*rg[2]);
}
void calc_rg_av(double **_rg)
{
int i, j, k, p;
double dx,dy,dz, r_CM_x,r_CM_y,r_CM_z;
double r_G=0.0,r_G2=0.0, r_G4=0.0;
double *rg=NULL, IdoubMPC, tmp;
double M;
*_rg = rg = realloc(rg,4*sizeof(double));
IdoubMPC = 1./(double)chain_length;
for (k=0; k<n_configs; k++) {
for (i=0; i<chain_n_chains; i++) {
M=0.0;
r_CM_x = r_CM_y = r_CM_z = 0.0;
for (j=0; j<chain_length; j++) {
p = chain_start+i*chain_length + j;
r_CM_x += configs[k][3*p]*PMASS(partCfg[p]);
r_CM_y += configs[k][3*p + 1]*PMASS(partCfg[p]);
r_CM_z += configs[k][3*p + 2]*PMASS(partCfg[p]);
M += PMASS(partCfg[p]);
}
r_CM_x /= M; r_CM_y /= M; r_CM_z /= M;
tmp = 0.0;
for (j=0; j<chain_length; ++j) {
p = chain_start+i*chain_length + j;
dx = configs[k][3*p] - r_CM_x;
dy = configs[k][3*p + 1] - r_CM_y;
dz = configs[k][3*p + 2] - r_CM_z;
tmp += (SQR(dx) + SQR(dy) + SQR(dz));
}
tmp *= IdoubMPC;
r_G += sqrt(tmp);
r_G2 += tmp;
r_G4 += tmp*tmp;
}
}
tmp = (double)(chain_n_chains*n_configs);
rg[0] = r_G/tmp;
rg[2] = r_G2/tmp;
rg[1] = sqrt(rg[2] - rg[0]*rg[0]);
rg[3] = sqrt(r_G4/tmp - rg[2]*rg[2]);
}
void calc_rh(double **_rh)
{
int i, j, p;
double dx,dy,dz, r_H=0.0,r_H2=0.0, *rh=NULL, ri=0.0, prefac, tmp;
*_rh = rh = realloc(rh,2*sizeof(double));
prefac = 0.5*chain_length*chain_length; /* 1/N^2 is not a normalization factor */
for(p=0;p<chain_n_chains;p++) {
ri=0.0;
for(i=chain_start+chain_length*p;i<chain_start+chain_length*(p+1);i++) {
for(j=i+1;j<chain_start+chain_length*(p+1);j++) {
dx = partCfg[i].r.p[0]-partCfg[j].r.p[0]; dx*=dx;
dy = partCfg[i].r.p[1]-partCfg[j].r.p[1]; dy*=dy;
dz = partCfg[i].r.p[2]-partCfg[j].r.p[2]; dz*=dz;
ri += 1.0/sqrt(dx+dy+dz);
}
}
tmp = prefac/ri;
r_H += tmp;
r_H2 += tmp*tmp;
}
tmp = (double)chain_n_chains;
rh[0] = r_H/tmp;
rh[1] = sqrt(r_H2/tmp - rh[0]*rh[0]);
}
void calc_rh_av(double **_rh)
{
int i, j, p, k;
double dx,dy,dz, r_H=0.0,r_H2=0.0, *rh=NULL, ri=0.0, prefac, tmp;
*_rh = rh = realloc(rh,2*sizeof(double));
prefac = 0.5*chain_length*chain_length;
for(k=0; k<n_configs; k++) {
for(p=0;p<chain_n_chains;p++) {
ri=0.0;
for(i=chain_start+chain_length*p;i<chain_start+chain_length*(p+1);i++) {
for(j=i+1;j<chain_start+chain_length*(p+1);j++) {
dx = configs[k][3*i] -configs[k][3*j];
dy = configs[k][3*i+1]-configs[k][3*j+1];
dz = configs[k][3*i+2]-configs[k][3*j+2];
ri += 1.0/sqrt(dx*dx + dy*dy + dz*dz);
}
}
tmp = prefac/ri;
r_H += tmp;
r_H2 += tmp*tmp;
}
}
tmp = (double)chain_n_chains*n_configs;
rh[0] = r_H/tmp;
rh[1] = sqrt(r_H2/tmp - rh[0]*rh[0]);
}
void calc_internal_dist(double **_idf) {
int i,j,k;
double dx,dy,dz;
double *idf=NULL;
*_idf = idf = realloc(idf,chain_length*sizeof(double));
idf[0] = 0.0;
for (k=1; k < chain_length; k++) {
idf[k] = 0.0;
for (i=0; i<chain_n_chains; i++) {
for (j=0; j < chain_length-k; j++) {
dx = partCfg[chain_start+i*chain_length + j+k].r.p[0]
- partCfg[chain_start+i*chain_length + j].r.p[0];
dy = partCfg[chain_start+i*chain_length + j+k].r.p[1]
- partCfg[chain_start+i*chain_length + j].r.p[1];
dz = partCfg[chain_start+i*chain_length + j+k].r.p[2]
- partCfg[chain_start+i*chain_length +j].r.p[2];
idf[k] += (SQR(dx) + SQR(dy) + SQR(dz));
}
}
idf[k] = sqrt(idf[k] / (1.0*(chain_length-k)*chain_n_chains));
}
}
void calc_internal_dist_av(double **_idf) {
int i,j,k,n, i1,i2;
double dx,dy,dz;
double *idf=NULL;
*_idf = idf = realloc(idf,chain_length*sizeof(double));
idf[0] = 0.0;
for (k=1; k < chain_length; k++) {
idf[k] = 0.0;
for (n=0; n<n_configs; n++) {
for (i=0; i<chain_n_chains; i++) {
for (j=0; j < chain_length-k; j++) {
i2 = chain_start+i*chain_length + j; i1 = i2 + k;
dx = configs[n][3*i1] - configs[n][3*i2];
dy = configs[n][3*i1+1] - configs[n][3*i2+1];
dz = configs[n][3*i1+2] - configs[n][3*i2+2];
idf[k] += (SQR(dx) + SQR(dy) + SQR(dz));
}
}
}
idf[k] = sqrt(idf[k] / (1.0*(chain_length-k)*chain_n_chains*n_configs));
}
}
void calc_bond_l(double **_bond_l) {
int i,j;
double dx,dy,dz, tmp;
double *bond_l=NULL;
*_bond_l = bond_l = realloc(bond_l,4*sizeof(double));
bond_l[0] = bond_l[1] = bond_l[2] = 0.0; bond_l[3] = 20.0;
for (i=0; i<chain_n_chains; i++) {
for (j=0; j < chain_length-1; j++) {
dx = partCfg[chain_start+i*chain_length + j+1].r.p[0]
- partCfg[chain_start+i*chain_length + j].r.p[0];
dy = partCfg[chain_start+i*chain_length + j+1].r.p[1]
- partCfg[chain_start+i*chain_length + j].r.p[1];
dz = partCfg[chain_start+i*chain_length + j+1].r.p[2]
- partCfg[chain_start+i*chain_length +j].r.p[2];
tmp = SQR(dx) + SQR(dy) + SQR(dz);
bond_l[0] += sqrt(tmp);
bond_l[1] += tmp;
if (tmp > bond_l[2]) {bond_l[2] = tmp;}
if (tmp < bond_l[3]) {bond_l[3] = tmp;}
}
}
tmp = (double)(chain_length-1)*chain_n_chains;
bond_l[0] = bond_l[0] / tmp;
bond_l[1] = sqrt(bond_l[1]/tmp - SQR(bond_l[0]));
bond_l[2] = sqrt(bond_l[2]);
bond_l[3] = sqrt(bond_l[3]);
}
void calc_bond_l_av(double **_bond_l) {
int i,j,n, i1,i2;
double dx,dy,dz, tmp;
double *bond_l=NULL;
*_bond_l = bond_l = realloc(bond_l,4*sizeof(double));
bond_l[0] = bond_l[1] = bond_l[2] = 0.0; bond_l[3] = 20.0;
for (n=0; n<n_configs; n++) {
for (i=0; i<chain_n_chains; i++) {
for (j=0; j < chain_length-1; j++) {
i2 = chain_start+i*chain_length + j; i1 = i2 + 1;
dx = configs[n][3*i1] - configs[n][3*i2];
dy = configs[n][3*i1+1] - configs[n][3*i2+1];
dz = configs[n][3*i1+2] - configs[n][3*i2+2];
tmp = SQR(dx) + SQR(dy) + SQR(dz);
bond_l[0] += sqrt(tmp);
bond_l[1] += tmp;
if (tmp > bond_l[2]) {bond_l[2] = tmp;}
if (tmp < bond_l[3]) {bond_l[3] = tmp;}
}
}
}
tmp = (double)(chain_length-1)*chain_n_chains*n_configs;
bond_l[0] = bond_l[0] / tmp;
bond_l[1] = sqrt(bond_l[1]/tmp - SQR(bond_l[0]));
bond_l[2] = sqrt(bond_l[2]);
bond_l[3] = sqrt(bond_l[3]);
}
void calc_bond_dist(double **_bdf, int ind_n) {
int i,j=ind_n,k;
double dx,dy,dz;
double *bdf=NULL;
*_bdf = bdf = realloc(bdf,chain_length*sizeof(double));
bdf[0] = 0.0;
for (k=1; k < chain_length; k++) {
bdf[k] = 0.0;
for (i=0; i<chain_n_chains; i++) {
if (j < chain_length-k) {
dx = partCfg[chain_start+i*chain_length + j+k].r.p[0]
- partCfg[chain_start+i*chain_length + j].r.p[0];
dy = partCfg[chain_start+i*chain_length + j+k].r.p[1]
- partCfg[chain_start+i*chain_length + j].r.p[1];
dz = partCfg[chain_start+i*chain_length + j+k].r.p[2]
- partCfg[chain_start+i*chain_length +j].r.p[2];
bdf[k] += (SQR(dx) + SQR(dy) + SQR(dz));
}
}
bdf[k] = sqrt(bdf[k] / (1.0*chain_n_chains));
}
}
void calc_bond_dist_av(double **_bdf, int ind_n) {
int i,j=ind_n,k,n, i1,i2;
double dx,dy,dz;
double *bdf=NULL;
*_bdf = bdf = realloc(bdf,chain_length*sizeof(double));
bdf[0] = 0.0;
for (k=1; k < chain_length; k++) {
bdf[k] = 0.0;
for (n=0; n<n_configs; n++) {
for (i=0; i<chain_n_chains; i++) {
if (j < chain_length-k) {
i2 = chain_start+i*chain_length + j; i1 = i2 + k;
dx = configs[n][3*i1] - configs[n][3*i2];
dy = configs[n][3*i1+1] - configs[n][3*i2+1];
dz = configs[n][3*i1+2] - configs[n][3*i2+2];
bdf[k] += (SQR(dx) + SQR(dy) + SQR(dz));
}
}
}
bdf[k] = sqrt(bdf[k] / (1.0*chain_n_chains*n_configs));
}
}
void init_g123()
{
int i, j, p;
double cm_tmp[3], M;
/* Save particles' current positions
(which'll be used as initial position later on) */
partCoord_g = (float *) realloc(partCoord_g, 3*n_total_particles*sizeof(float));
partCM_g = (float *) realloc(partCM_g, 3*chain_n_chains*sizeof(float));
n_part_g = n_total_particles;
n_chains_g = chain_n_chains;
for(j=0; j<chain_n_chains; j++) {
cm_tmp[0] = cm_tmp[1] = cm_tmp[2] = 0.0;
M=0.0;
for(i=0; i<chain_length; i++) {
p = chain_start+j*chain_length + i;
partCoord_g[3*p] = partCfg[p].r.p[0]; cm_tmp[0]+=partCfg[p].r.p[0]*PMASS(partCfg[p]);
partCoord_g[3*p+1] = partCfg[p].r.p[1]; cm_tmp[1]+=partCfg[p].r.p[1]*PMASS(partCfg[p]);
partCoord_g[3*p+2] = partCfg[p].r.p[2]; cm_tmp[2]+=partCfg[p].r.p[2]*PMASS(partCfg[p]);
M += PMASS(partCfg[p]);
}
partCM_g[3*j] = cm_tmp[0]/M;
partCM_g[3*j+1] = cm_tmp[1]/M;
partCM_g[3*j+2] = cm_tmp[2]/M;
}
}
void calc_g123(double *_g1, double *_g2, double *_g3)
{
/* - Mean square displacement of a monomer
- Mean square displacement in the center of gravity of the chain itself
- Motion of the center of mass */
int i, j, p;
double g1=0.0, g2=0.0, g3=0.0, cm_tmp[3];
double M;
for(j=0; j<chain_n_chains; j++) {
cm_tmp[0] = cm_tmp[1] = cm_tmp[2] = 0.0;
M=0.0;
for(i=0; i<chain_length; i++) {
p = chain_start+j*chain_length + i;
cm_tmp[0]+=partCfg[p].r.p[0]*PMASS(partCfg[p]);
cm_tmp[1]+=partCfg[p].r.p[1]*PMASS(partCfg[p]);
cm_tmp[2]+=partCfg[p].r.p[2]*PMASS(partCfg[p]);
M += PMASS(partCfg[p]);
}
cm_tmp[0] /= M;
cm_tmp[1] /= M;
cm_tmp[2] /= M;
for(i=0; i<chain_length; i++) {
p = chain_start+j*chain_length + i;
g1 += SQR(partCfg[p].r.p[0]-partCoord_g[3*p])
+ SQR(partCfg[p].r.p[1]-partCoord_g[3*p+1])
+ SQR(partCfg[p].r.p[2]-partCoord_g[3*p+2]);
g2 += SQR( (partCfg[p].r.p[0]-partCoord_g[3*p])
- (cm_tmp[0]-partCM_g[3*j] ) )
+ SQR( (partCfg[p].r.p[1]-partCoord_g[3*p+1])
- (cm_tmp[1]-partCM_g[3*j+1]) )
+ SQR( (partCfg[p].r.p[2]-partCoord_g[3*p+2])
- (cm_tmp[2]-partCM_g[3*j+2]) );
}
g3 += SQR(cm_tmp[0]-partCM_g[3*j])
+ SQR(cm_tmp[1]-partCM_g[3*j+1])
+ SQR(cm_tmp[2]-partCM_g[3*j+2]);
}
*_g1 = g1 / (1.*chain_n_chains*chain_length);
*_g2 = g2 / (1.*chain_n_chains*chain_length);
*_g3 = g3 / (1.*chain_n_chains);
}
void calc_g1_av(double **_g1, int window, double weights[3]) {
int i, j, p, t,k, cnt;
double *g1=NULL;
*_g1 = g1 = realloc(g1,n_configs*sizeof(double));
for(k=0; k < n_configs; k++) {
g1[k] = 0.0;
cnt = window?n_configs-k:1;
for(t=window?0:n_configs-k-1; t < n_configs-k; t++) {
for(j=0; j<chain_n_chains; j++) {
for(i=0; i<chain_length; i++) {
p = chain_start+j*chain_length + i;
g1[k] += weights[0]*SQR(configs[t+k][3*p]-configs[t][3*p])
+ weights[1]*SQR(configs[t+k][3*p+1]-configs[t][3*p+1])
+ weights[2]*SQR(configs[t+k][3*p+2]-configs[t][3*p+2]);
}
}
}
g1[k] /= ((double)chain_n_chains*chain_length*cnt);
}
}
void calc_g2_av(double **_g2, int window, double weights[3]) {
int i, j, p, t,k,cnt;
double *g2=NULL, cm_tmp[3];
double M;
*_g2 = g2 = realloc(g2,n_configs*sizeof(double));
for(k=0; k < n_configs; k++) {
g2[k] = 0.0;
cnt = window?n_configs-k:1;
for(t=window?0:n_configs-k-1; t < n_configs-k; t++) {
for(j=0; j<chain_n_chains; j++) {
cm_tmp[0] = cm_tmp[1] = cm_tmp[2] = 0.0;
M=0.0;
for(i=0; i<chain_length; i++) {
p = chain_start+j*chain_length + i;
cm_tmp[0] += (configs[t+k][3*p] - configs[t][3*p])*PMASS(partCfg[p]);
cm_tmp[1] += (configs[t+k][3*p+1] - configs[t][3*p+1])*PMASS(partCfg[p]);
cm_tmp[2] += (configs[t+k][3*p+2] - configs[t][3*p+2])*PMASS(partCfg[p]);
M += PMASS(partCfg[p]);
}
cm_tmp[0] /= M; cm_tmp[1] /= M; cm_tmp[2] /= M;
for(i=0; i<chain_length; i++) {
p = chain_start+j*chain_length + i;
g2[k] += weights[0]*SQR( (configs[t+k][3*p]-configs[t][3*p]) - cm_tmp[0] )
+ weights[1]*SQR( (configs[t+k][3*p+1]-configs[t][3*p+1]) - cm_tmp[1] )
+ weights[2]*SQR( (configs[t+k][3*p+2]-configs[t][3*p+2]) - cm_tmp[2] );
}
}
}
g2[k] /= ((double)chain_n_chains*chain_length*cnt);
}
}
void calc_g3_av(double **_g3, int window, double weights[3]) {
int i, j, p, t,k,cnt;
double *g3=NULL, cm_tmp[3];
double M;
*_g3 = g3 = realloc(g3,n_configs*sizeof(double));
for(k=0; k < n_configs; k++) {
g3[k] = 0.0;
cnt = window?n_configs-k:1;
for(t=window?0:n_configs-k-1; t < n_configs-k; t++) {
for(j=0; j<chain_n_chains; j++) {
cm_tmp[0] = cm_tmp[1] = cm_tmp[2] = 0.0;
M=0.0;
for(i=0; i<chain_length; i++) {
p = chain_start+j*chain_length + i;
cm_tmp[0] += (configs[t+k][3*p] - configs[t][3*p])*PMASS(partCfg[p]);
cm_tmp[1] += (configs[t+k][3*p+1] - configs[t][3*p+1])*PMASS(partCfg[p]);
cm_tmp[2] += (configs[t+k][3*p+2] - configs[t][3*p+2])*PMASS(partCfg[p]);
M += PMASS(partCfg[p]);
}
g3[k] += (weights[0]*SQR(cm_tmp[0]) + weights[1]*SQR(cm_tmp[1]) + weights[2]*SQR(cm_tmp[2]))/SQR(M);
}
}
g3[k] /= ((double)chain_n_chains*cnt);
}
}
void analyze_formfactor(double qmin, double qmax, int qbins, double **_ff) {
int i,j,k,qi, cnt,cnt_max;
double q,qfak, qr, dx,dy,dz, *r_ij=NULL, *ff=NULL;
*_ff = ff = realloc(ff,(qbins+1)*sizeof(double));
r_ij = realloc(r_ij,chain_length*(chain_length-1)/2*sizeof(double));
qfak = pow((qmax/qmin),(1.0/qbins));
for(qi=0; qi<=qbins; qi++) ff[qi] = 0.0;
for(k=0; k < chain_n_chains; k++) {
cnt = 0;
/* Prepare distance matrice r_ij for current chain k */
for(i=chain_start+k*chain_length; i<chain_start+(k+1)*chain_length; i++) {
for(j=i+1; j<chain_start+(k+1)*chain_length;j++) {
dx = partCfg[i].r.p[0]-partCfg[j].r.p[0]; dx*=dx;
dy = partCfg[i].r.p[1]-partCfg[j].r.p[1]; dy*=dy;
dz = partCfg[i].r.p[2]-partCfg[j].r.p[2]; dz*=dz;
r_ij[cnt++] = sqrt(dx + dy + dz);
}
}
q = qmin; cnt_max = cnt;
/* Derive spherically averaged S(q) = 1/chain_length * Sum(i,j=1..chain_length)[sin(q*r_ij)/q*r_ij] for current chain k */
for(qi=0; qi<=qbins; qi++) {
ff[qi] += chain_length;
for(cnt=0; cnt<cnt_max; cnt++) {
qr = q*r_ij[cnt];
ff[qi] += 2*sin(qr)/qr;
}
q *= qfak;
}
}
for(qi=0; qi<=qbins; qi++) ff[qi] /= ((double)chain_length*chain_n_chains);
free(r_ij);
}
void analyze_formfactor_av(double qmin, double qmax, int qbins, double **_ff) {
int i,j,k,n,qi, cnt,cnt_max;
double q,qfak, qr, dx,dy,dz, *r_ij=NULL, *ff=NULL;
*_ff = ff = realloc(ff,(qbins+1)*sizeof(double));
r_ij = realloc(r_ij,chain_length*(chain_length-1)/2*sizeof(double));
qfak = pow((qmax/qmin),(1.0/qbins));
for(qi=0; qi<=qbins; qi++) ff[qi] = 0.0;
for(n=0; n < n_configs; n++) {
for(k=0; k < chain_n_chains; k++) {
cnt = 0;
/* Prepare distance matrice r_ij for current chain k of configuration n */
for(i=chain_start+k*chain_length; i<chain_start+(k+1)*chain_length; i++) {
for(j=i+1; j<chain_start+(k+1)*chain_length;j++) {
dx = configs[n][3*i] -configs[n][3*j]; dx*=dx;
dy = configs[n][3*i+1]-configs[n][3*j+1]; dy*=dy;
dz = configs[n][3*i+2]-configs[n][3*j+2]; dz*=dz;
r_ij[cnt++] = sqrt(dx + dy + dz);
}
}
q = qmin; cnt_max = cnt;
/* Derive spherically averaged S(q) = 1/chain_length * Sum(i,j=1..chain_length)[sin(q*r_ij)/q*r_ij] for current chain k */
for(qi=0; qi<=qbins; qi++) {
ff[qi] += chain_length;
for(cnt=0; cnt<cnt_max; cnt++) {
qr = q*r_ij[cnt];
ff[qi] += 2*sin(qr)/qr;
}
q *= qfak;
}
}
}
for(qi=0; qi<=qbins; qi++) ff[qi] /= ((double)chain_length*chain_n_chains*n_configs);
free(r_ij);
}
void analyze_rdfchain(double r_min, double r_max, int r_bins, double **_f1, double **_f2, double **_f3) {
int i, j, ind, c_i, c_j, mon;
double bin_width, inv_bin_width, factor, r_in, r_out, bin_volume, dist, chain_mass,
*cm=NULL, *min_d=NULL, *f1=NULL, *f2=NULL, *f3=NULL;
*_f1 = f1 = realloc(f1,r_bins*sizeof(double));
*_f2 = f2 = realloc(f2,r_bins*sizeof(double));
*_f3 = f3 = realloc(f3,r_bins*sizeof(double));
cm = realloc(cm,(chain_n_chains*3)*sizeof(double));
min_d = realloc(min_d,(chain_n_chains*chain_n_chains)*sizeof(double));
for(i=0; i<r_bins; i++) {
f1[i] = f2[i] = f3[i] = 0.0;
}
bin_width = (r_max-r_min) / (double)r_bins;
inv_bin_width = 1.0 / bin_width;
for(c_i=0; c_i<chain_n_chains; c_i++) {
cm[3*c_i] = cm[3*c_i+1] = cm[3*c_i+2] = 0.0;
for(c_j=(c_i+1); c_j<chain_n_chains; c_j++) {
min_d[c_i*chain_n_chains+c_j] = box_l[0] + box_l[1] + box_l[2];
}
}
for(c_i=0; c_i<chain_n_chains; c_i++) {
for(i=0; i<chain_length; i++) {
mon = chain_start + c_i*chain_length + i;
cm[3*c_i]+= partCfg[mon].r.p[0]*PMASS(partCfg[mon]);
cm[3*c_i+1]+= partCfg[mon].r.p[1]*PMASS(partCfg[mon]);
cm[3*c_i+2]+= partCfg[mon].r.p[2]*PMASS(partCfg[mon]);
for(c_j=(c_i+1); c_j<chain_n_chains; c_j++) {
for(j=0; j<chain_length; j++) {
dist = min_distance(partCfg[mon].r.p, partCfg[chain_start + c_j*chain_length+j].r.p);
if ((dist > r_min) && (dist < r_max)) {
ind = (int) ( (dist - r_min)*inv_bin_width );
f1[ind]+= 1.0;
}
if (dist<min_d[c_i*chain_n_chains+c_j]) min_d[c_i*chain_n_chains+c_j] = dist;
}
}
}
}
chain_mass = 0;
for(i=0; i<chain_length; i++) chain_mass+= PMASS(partCfg[i]);
for(c_i=0; c_i<chain_n_chains; c_i++) {
cm[3*c_i]/= chain_mass;
cm[3*c_i+1]/= chain_mass;
cm[3*c_i+2]/= chain_mass;
for(c_j=(c_i+1); c_j<chain_n_chains; c_j++) {
dist = min_d[c_i*chain_n_chains+c_j];
if ((dist > r_min) && (dist < r_max)) {
ind = (int) ( (dist - r_min)*inv_bin_width );
f3[ind]+= 1.0;
}
}
}
for(c_i=0; c_i<chain_n_chains; c_i++) {
for(c_j=(c_i+1); c_j<chain_n_chains; c_j++) {
dist = min_distance(&cm[3*c_i],&cm[3*c_j]);
if ((dist > r_min) && (dist < r_max)) {
ind = (int) ( (dist - r_min)*inv_bin_width );
f2[ind]+= 1.0;
}
}
}
/* normalization */
factor = box_l[0]*box_l[1]*box_l[2] *1.5/PI/(chain_n_chains*(chain_n_chains-1));
for(i=0; i<r_bins; i++) {
r_in = i*bin_width + r_min;
r_out = r_in + bin_width;
bin_volume = r_out*r_out*r_out - r_in*r_in*r_in;
f1[i] *= factor / (bin_volume * chain_length*chain_length);
f2[i] *= factor / bin_volume;
f3[i] *= factor / bin_volume;
}
}
#ifdef ELECTROSTATICS
void analyze_cwvac(int maxtau, int interval, double **_avac, double **_evac) {
int i,j,k,ic,n,mon,tau;
double *vac=NULL, *avac=NULL, *evac=NULL;
double *varr=NULL;
double vcm[3];
// result
vac = realloc(vac,(maxtau+1)*sizeof(double));
*_avac = avac = realloc(avac,(maxtau+1)*sizeof(double));
*_evac = evac = realloc(evac,(maxtau+1)*sizeof(double));
// set up velarray
varr = realloc(varr,(3*(n_configs-1)*n_total_particles)*sizeof(double));
// fill varr
for(k=0;k<n_configs-1;k++) {
for(i=0;i<n_total_particles;i++) {
for(j=0;j<3;j++) {
varr[k*3*n_total_particles+i*3+j]=configs[k+1][3*i+j]-configs[k][3*i+j];
}
}
}
// loop over chain
for(tau=0;tau<=maxtau;tau++) { avac[tau] = 0.0; evac[tau] = 0.0; }
for(n=0;n<chain_n_chains;n++) {
for(tau=0;tau<=maxtau;tau++) { vac[tau] = 0.0; }
// loop over configuration (interval)
for(ic=(n_configs-2);ic>=0;ic -= interval) {
if(ic < maxtau) break;
// calc center of mass velocity
vcm[0] = vcm[1] = vcm[2] = 0.0;
for(k=0;k<chain_length;k++) {
mon = chain_start+n*chain_length+k;
for(j=0;j<3;j++) {
vcm[j] += varr[ic*3*n_total_particles+mon*3+j];
}
}
for(j=0;j<3;j++) {
vcm[j] /= chain_length;
}
// loop over tau (maxtau)
for(tau=0;tau<=maxtau;tau++) {
// loop over particles
for(k=0;k<n_total_particles;k++) {
vac[tau] += partCfg[k].p.q*(
varr[(ic-tau)*3*n_total_particles+k*3 ]*vcm[0]
+ varr[(ic-tau)*3*n_total_particles+k*3+1]*vcm[1]
+ varr[(ic-tau)*3*n_total_particles+k*3+2]*vcm[2]);
}
}
}
// normalize vac and sum up to average
for(tau=0;tau<=maxtau;tau++) {
vac[tau] /= ((n_configs-maxtau)/interval);
avac[tau] += vac[tau];
evac[tau] += vac[tau]*vac[tau];
}
}
// normalize
// NOTE: normalization with time step and KbT has to be done on script level
for(tau=0;tau<=maxtau;tau++) {
evac[tau] = sqrt((evac[tau]-avac[tau]*avac[tau]/chain_n_chains)/(chain_n_chains*(chain_n_chains-1)));
avac[tau] /= chain_n_chains;
}
free(vac); free(varr);
}
#endif
/****************************************************************************************
* chain structure commands parsing
****************************************************************************************/
int parse_chain_structure_info(Tcl_Interp *interp, int argc, char **argv)
{
int m, i, pc;
/* 'analyze set chains <chain_start> <n_chains> <chain_length>' */
if (argc < 3) {
Tcl_AppendResult(interp, "chain structure info consists of <start> <n> <length>", (char *)NULL);
return TCL_ERROR;
}
if (! (ARG0_IS_I(chain_start) && ARG1_IS_I(chain_n_chains) && ARG_IS_I(2, chain_length)))
return TCL_ERROR;
realloc_topology(chain_n_chains);
pc = 0;
for (m = 0; m < n_molecules; m++) {
topology[m].type = 0;
realloc_intlist(&topology[m].part, topology[m].part.n = chain_length);
for (i = 0; i < chain_length; i++)
topology[m].part.e[i] = pc++;
}
return TCL_OK;
}
void update_mol_ids_setchains() {
Particle *p;
int i, np, c;
Cell *cell;
for (c = 0; c < local_cells.n; c++) {
cell = local_cells.cell[c];
p = cell->part;
np = cell->n;
for(i = 0; i < np; i++) {
p[i].p.mol_id = floor((p[i].p.identity - chain_start)/(double)chain_length);
}
}
}
int check_and_parse_chain_structure_info(Tcl_Interp *interp, int argc, char **argv)
{
if (argc > 0)
if (parse_chain_structure_info(interp, argc, argv) != TCL_OK)
return TCL_ERROR;
if (!sortPartCfg()) {
Tcl_AppendResult(interp, "for analyze, store particles consecutively starting with 0.",
(char *) NULL);
return (TCL_ERROR);
}
return TCL_OK;
}
int parse_re(Tcl_Interp *interp, int average, int argc, char **argv)
{
/* 'analyze { re | <re> } [<chain_start> <n_chains> <chain_length>]' */
char buffer[4*TCL_DOUBLE_SPACE+4];
double *re;
if (check_and_parse_chain_structure_info(interp, argc, argv) == TCL_ERROR)
return TCL_ERROR;
if ((argc != 0) && (argc != 3)) {
Tcl_AppendResult(interp, "only chain structure info required", (char *)NULL);
return TCL_ERROR;
}
if (!average)
calc_re(&re);
else {
if (n_configs == 0) {
Tcl_AppendResult(interp, "no configurations found! ", (char *)NULL);
Tcl_AppendResult(interp, "Use 'analyze append' to save some, or 'analyze re' to only look at current state!", (char *)NULL);
return TCL_ERROR;
}
calc_re_av(&re);
}
sprintf(buffer,"%f %f %f %f",re[0],re[1],re[2],re[3]);
Tcl_AppendResult(interp, buffer, (char *)NULL);
free(re);
return (TCL_OK);
}
int parse_rg(Tcl_Interp *interp, int average, int argc, char **argv)
{
/* 'analyze { rg | <rg> } [<chain_start> <n_chains> <chain_length>]' */
char buffer[4*TCL_DOUBLE_SPACE+4];
double *rg;
if (check_and_parse_chain_structure_info(interp, argc, argv) == TCL_ERROR)
return TCL_ERROR;
if ((argc != 0) && (argc != 3)) {
Tcl_AppendResult(interp, "only chain structure info required", (char *)NULL);
return TCL_ERROR;
}
if (!average)
calc_rg(&rg);
else {
if (n_configs == 0) {
Tcl_AppendResult(interp, "no configurations found! ", (char *)NULL);
Tcl_AppendResult(interp, "Use 'analyze append' to save some, or 'analyze rg' to only look at current state!", (char *)NULL);
return TCL_ERROR;
}
calc_rg_av(&rg);
}
sprintf(buffer,"%f %f %f %f",rg[0],rg[1],rg[2],rg[3]);
Tcl_AppendResult(interp, buffer, (char *)NULL);
free(rg);
return (TCL_OK);
}
int parse_rh(Tcl_Interp *interp, int average, int argc, char **argv)
{
/* 'analyze { rh | <rh> } [<chain_start> <n_chains> <chain_length>]' */
char buffer[2*TCL_DOUBLE_SPACE+2];
double *rh;
if (check_and_parse_chain_structure_info(interp, argc, argv) == TCL_ERROR)
return TCL_ERROR;
if ((argc != 0) && (argc != 3)) {
Tcl_AppendResult(interp, "only chain structure info required", (char *)NULL);
return TCL_ERROR;
}
if (!average)
calc_rh(&rh);
else {
if (n_configs == 0) {
Tcl_AppendResult(interp, "no configurations found! ", (char *)NULL);
Tcl_AppendResult(interp, "Use 'analyze append' to save some, or 'analyze rh' to only look at current state!", (char *)NULL);
return TCL_ERROR;
}
else
calc_rh_av(&rh);
}
sprintf(buffer,"%f %f",rh[0],rh[1]);
Tcl_AppendResult(interp, buffer, (char *)NULL);
free(rh);
return (TCL_OK);
}
int parse_intdist(Tcl_Interp *interp, int average, int argc, char **argv)
{
/* 'analyze { internal_dist | <internal_dist> } [<chain_start> <n_chains> <chain_length>]' */
char buffer[TCL_DOUBLE_SPACE+2];
int i;
double *idf;
if (check_and_parse_chain_structure_info(interp, argc, argv) == TCL_ERROR) return TCL_ERROR;
if ((argc != 0) && (argc != 3)) { Tcl_AppendResult(interp, "only chain structure info required", (char *)NULL); return TCL_ERROR; }
if (!average)
calc_internal_dist(&idf);
else {
if (n_configs == 0) {
Tcl_AppendResult(interp, "no configurations found! ", (char *)NULL);
Tcl_AppendResult(interp, "Use 'analyze append' to save some, or 'analyze internal_dist' to only look at current state!", (char *)NULL);
return TCL_ERROR;
}
else
calc_internal_dist_av(&idf);
}
for (i=0; i<chain_length; i++) {
sprintf(buffer,"%f ",idf[i]); Tcl_AppendResult(interp, buffer, (char *)NULL);
}
free(idf);
return (TCL_OK);
}
int parse_bond_l(Tcl_Interp *interp, int average, int argc, char **argv)
{
/* 'analyze { bond_l | <bond_l> } [<chain_start> <n_chains> <chain_length>]' */
/*****************************************************************************/
char buffer[4*TCL_DOUBLE_SPACE+4];
double *bond_l;
if (check_and_parse_chain_structure_info(interp, argc, argv) == TCL_ERROR) return TCL_ERROR;
if ((argc != 0) && (argc != 3)) { Tcl_AppendResult(interp, "only chain structure info required", (char *)NULL); return TCL_ERROR; }
if (!average) calc_bond_l(&bond_l);
else if (n_configs == 0) {
Tcl_AppendResult(interp, "no configurations found! ", (char *)NULL);
Tcl_AppendResult(interp, "Use 'analyze append' to save some, or 'analyze bond_l' to only look at current state!", (char *)NULL);
return TCL_ERROR; }
else calc_bond_l_av(&bond_l);
sprintf(buffer,"%f %f %f %f",bond_l[0],bond_l[1],bond_l[2],bond_l[3]); Tcl_AppendResult(interp, buffer, (char *)NULL);
free(bond_l);
return (TCL_OK);
}
int parse_bond_dist(Tcl_Interp *interp, int average, int argc, char **argv)
{
/* 'analyze { bond_dist | <bond_dist> } [index <index>] [<chain_start> <n_chains> <chain_length>]' */
/***************************************************************************************************/
char buffer[TCL_INTEGER_SPACE + TCL_DOUBLE_SPACE+2];
double *bdf; int ind_n=0, i;
if (argc >= 1 && !strncmp(argv[0], "index", strlen(argv[0]))) { ind_n = atoi(argv[1]); argc-=2; argv+=2; }
if (check_and_parse_chain_structure_info(interp, argc, argv) == TCL_ERROR) return TCL_ERROR;
if ((argc != 0) && (argc != 3)) { Tcl_AppendResult(interp, "only chain structure info required", (char *)NULL); return TCL_ERROR; }
if (ind_n < 0 || ind_n > chain_length-1) {
sprintf(buffer,"%d!",chain_length-1);
Tcl_AppendResult(interp, "ERROR: <index> must be between 0 and ", buffer, (char *)NULL); return TCL_ERROR; }
if (ind_n >= chain_length/2) ind_n = (chain_length-1) - ind_n;
if (!average) calc_bond_dist(&bdf,ind_n);
else if (n_configs == 0) {
Tcl_AppendResult(interp, "no configurations found! ", (char *)NULL);
Tcl_AppendResult(interp, "Use 'analyze append' to save some, or 'analyze internal_dist' to only look at current state!", (char *)NULL);
return TCL_ERROR; }
else calc_bond_dist_av(&bdf,ind_n);
for (i=0; i<chain_length-ind_n; i++) {
sprintf(buffer,"%f ",bdf[i]); Tcl_AppendResult(interp, buffer, (char *)NULL);
}
free(bdf);
return (TCL_OK);
}
int parse_g123(Tcl_Interp *interp, int average, int argc, char **argv)
{
/* 'analyze g123 [-init] [<chain_start> <n_chains> <chain_length>]' */
/********************************************************************/
char buffer[3*TCL_DOUBLE_SPACE+7];
int init = 0;
double g1, g2, g3;
if (argc > 0 && ARG0_IS_S("-init")) {
init = 1; argc--; argv++;
}
if (check_and_parse_chain_structure_info(interp, argc, argv) == TCL_ERROR)
return TCL_ERROR;
if ((argc != 0) && (argc != 3)) { Tcl_AppendResult(interp, "only chain structure info required", (char *)NULL); return TCL_ERROR; }
if (init) { init_g123(); return TCL_OK; }
if (partCoord_g == NULL || partCM_g == NULL) {