From fedf2b217113800a15f367e111e2dbcad4a3c92c Mon Sep 17 00:00:00 2001
From: Miha <mihaf@hapi.(none)>
Date: Thu, 06 Feb 2014 17:39:37 +0000
Subject: [PATCH] Polymers thermicaly move now! HArmonic potential added.
---
src/io.c | 95 +++++++++++++++++++++++++++++++++++++++++------
1 files changed, 83 insertions(+), 12 deletions(-)
diff --git a/src/io.c b/src/io.c
index 7421f0d..8b51793 100644
--- a/src/io.c
+++ b/src/io.c
@@ -8,7 +8,8 @@
#include<stdlib.h>
#include <sys/types.h>
#include <dirent.h>
-
+#include "initial_distribution.h"
+#include "poly.h"
ts_bool print_vertex_list(ts_vertex_list *vlist){
ts_uint i;
@@ -206,7 +207,7 @@
ts_vertex_list *vlist=vesicle->vlist;
ts_bond_list *blist=vesicle->blist;
ts_vertex **vtx=vlist->vtx;
- ts_uint i;
+ ts_uint i,j;
char filename[255];
FILE *fh;
@@ -217,29 +218,69 @@
return TS_FAIL;
}
/* Here comes header of the file */
+
+ //find number of extra vtxs and bonds of polymeres
+ ts_uint monono=0, polyno=0;
+ ts_bool poly=0;
+ if(vesicle->poly_list!=NULL){
+ if(vesicle->poly_list->poly[0]!=NULL){
+ polyno=vesicle->poly_list->n;
+ monono=vesicle->poly_list->poly[0]->vlist->n;
+ poly=1;
+ }
+ }
fprintf(fh, "<?xml version=\"1.0\"?>\n<VTKFile type=\"UnstructuredGrid\" version=\"0.1\" byte_order=\"LittleEndian\" compressor=\"vtkZLibDataCompressor\">\n <UnstructuredGrid>\n");
- fprintf(fh, "<Piece NumberOfPoints=\"%u\" NumberOfCells=\"%u\">\n",vlist->n, blist->n);
+ fprintf(fh, "<Piece NumberOfPoints=\"%u\" NumberOfCells=\"%u\">\n",vlist->n+monono*polyno, blist->n+monono*polyno);
fprintf(fh,"<PointData Scalars=\"scalars\">\n<DataArray type=\"Int64\" Name=\"scalars\" format=\"ascii\">");
for(i=0;i<vlist->n;i++){
fprintf(fh,"%u ",vtx[i]->idx);
}
+ //polymeres
+ if(poly){
+ for(i=0;i<vesicle->poly_list->n;i++){
+ for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++){
+ fprintf(fh,"%u ", vesicle->poly_list->poly[i]->vlist->vtx[j]->idx);
+ }
+ }
+ }
fprintf(fh,"</DataArray>\n</PointData>\n<CellData>\n</CellData>\n<Points>\n<DataArray type=\"Float64\" Name=\"Koordinate tock\" NumberOfComponents=\"3\" format=\"ascii\">\n");
for(i=0;i<vlist->n;i++){
fprintf(fh,"%e %e %e\n",vtx[i]->x,vtx[i]->y, vtx[i]->z);
+ }
+ //polymeres
+ if(poly){
+ for(i=0;i<vesicle->poly_list->n;i++){
+ for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++){
+ fprintf(fh,"%e %e %e\n", vesicle->poly_list->poly[i]->vlist->vtx[j]->x,vesicle->poly_list->poly[i]->vlist->vtx[j]->y, vesicle->poly_list->poly[i]->vlist->vtx[j]->z );
+ }
+ }
}
fprintf(fh,"</DataArray>\n</Points>\n<Cells>\n<DataArray type=\"Int64\" Name=\"connectivity\" format=\"ascii\">");
for(i=0;i<blist->n;i++){
fprintf(fh,"%u %u\n",blist->bond[i]->vtx1->idx,blist->bond[i]->vtx2->idx);
}
+ //polymeres
+ if(poly){
+ for(i=0;i<vesicle->poly_list->n;i++){
+ for(j=0;j<vesicle->poly_list->poly[i]->blist->n;j++){
+ fprintf(fh,"%u %u\n", vesicle->poly_list->poly[i]->blist->bond[j]->vtx1->idx,vesicle->poly_list->poly[i]->blist->bond[j]->vtx2->idx);
+ }
+ //grafted bonds
+ fprintf(fh,"%u %u\n", vesicle->poly_list->poly[i]->grafted_vtx->idx, vesicle->poly_list->poly[i]->vlist->vtx[0]->idx);
+ }
+
+ }
+
+
fprintf(fh,"</DataArray>\n<DataArray type=\"Int64\" Name=\"offsets\" format=\"ascii\">");
- for (i=2;i<blist->n*2+1;i+=2){
+ for (i=2;i<(blist->n+monono*polyno)*2+1;i+=2){
fprintf(fh,"%u ",i);
}
fprintf(fh,"\n");
fprintf(fh,"</DataArray>\n<DataArray type=\"UInt8\" Name=\"types\" format=\"ascii\">\n");
- for (i=0;i<blist->n;i++){
+ for (i=0;i<blist->n+monono*polyno;i++){
fprintf(fh,"3 ");
}
@@ -294,20 +335,35 @@
-ts_bool parsetape(ts_vesicle *vesicle,ts_uint *iterations){
- long int nshell=17,ncxmax=60, ncymax=60, nczmax=60; // THIS IS DUE TO CONFUSE BUG!
- ts_double xk0=25.0, dmax=1.67,stepsize=0.15;
- *iterations=1000;
+ts_vesicle *parsetape(ts_uint *mcsweeps, ts_uint *inititer, ts_uint *iterations){
+ long int nshell=17,ncxmax=60, ncymax=60, nczmax=60, npoly=10, nmono=20; // THIS IS DUE TO CONFUSE BUG!
+ char *buf=malloc(255*sizeof(char));
+ long int brezveze0=1;
+ long int brezveze1=1;
+ long int brezveze2=1;
+ ts_double xk0=25.0, dmax=1.67,stepsize=0.15,kspring=800.0;
+ long int iter=1000, init=1000, mcsw=1000;
+
+
cfg_opt_t opts[] = {
CFG_SIMPLE_INT("nshell", &nshell),
+ CFG_SIMPLE_INT("npoly", &npoly),
+ CFG_SIMPLE_INT("nmono", &nmono),
CFG_SIMPLE_FLOAT("dmax", &dmax),
CFG_SIMPLE_FLOAT("xk0",&xk0),
+ CFG_SIMPLE_FLOAT("k_spring",&kspring),
CFG_SIMPLE_FLOAT("stepsize",&stepsize),
CFG_SIMPLE_INT("nxmax", &ncxmax),
CFG_SIMPLE_INT("nymax", &ncymax),
CFG_SIMPLE_INT("nzmax", &nczmax),
- CFG_SIMPLE_INT("iterations",iterations),
+ CFG_SIMPLE_INT("iterations",&iter),
+ CFG_SIMPLE_INT("mcsweeps",&mcsw),
+ CFG_SIMPLE_INT("inititer", &init),
CFG_SIMPLE_BOOL("quiet",&quiet),
+ CFG_SIMPLE_STR("multiprocessing",buf),
+ CFG_SIMPLE_INT("smp_cores",&brezveze0),
+ CFG_SIMPLE_INT("cluster_nodes",&brezveze1),
+ CFG_SIMPLE_INT("distributed_processes",&brezveze2),
CFG_END()
};
cfg_t *cfg;
@@ -320,6 +376,16 @@
else if(retval==CFG_PARSE_ERROR){
fatal("Invalid tape!",100);
}
+ ts_vesicle *vesicle;
+ *iterations=iter;
+ *inititer=init;
+ *mcsweeps=mcsw;
+ vesicle=initial_distribution_dipyramid(nshell,ncxmax,ncymax,nczmax,stepsize);
+ vesicle->poly_list=init_poly_list(npoly,nmono, vesicle->vlist);
+ vesicle->spring_constant=kspring;
+ poly_assign_spring_const(vesicle);
+
+
vesicle->nshell=nshell;
vesicle->dmax=dmax*dmax;
vesicle->bending_rigidity=xk0;
@@ -328,9 +394,14 @@
vesicle->clist->ncmax[1]=ncymax;
vesicle->clist->ncmax[2]=nczmax;
vesicle->clist->max_occupancy=8;
+
cfg_free(cfg);
-// fprintf(stderr,"NSHELL=%u\n",vesicle->nshell);
- return TS_SUCCESS;
+ free(buf);
+ // fprintf(stderr,"NSHELL=%u\n",vesicle->nshell);
+
+
+
+ return vesicle;
}
--
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