From 06afc729f9061c1cfa14c78728d61d518324c2f0 Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@gmail.com>
Date: Wed, 04 May 2022 05:46:43 +0000
Subject: [PATCH] Moved all global variables to separate file and defined extern keyword where appropriate
---
src/io.c | 87 +++++++++++++++++++++++++++++++++----------
1 files changed, 66 insertions(+), 21 deletions(-)
diff --git a/src/io.c b/src/io.c
index 65a426b..a331c44 100644
--- a/src/io.c
+++ b/src/io.c
@@ -1,6 +1,7 @@
/* vim: set ts=4 sts=4 sw=4 noet : */
#include "general.h"
+#include "globals.h"
#include<stdio.h>
#include "io.h"
#include "vertex.h"
@@ -424,7 +425,8 @@
vesicle->tape=parsetape(command_line_args.tape_fullfilename);
// recreating space for cells //
vesicle->clist=init_cell_list(vesicle->tape->ncxmax, vesicle->tape->ncymax, vesicle->tape->nczmax, vesicle->tape->stepsize);
- vesicle->clist->max_occupancy=16;
+//THIS IS HARDCODED IN CELL.C NOW
+// vesicle->clist->max_occupancy=16;
// vesicle->tape=(ts_tape *)malloc(sizeof(ts_tape));
// retval=fread(vesicle->tape, sizeof(ts_tape),1,fh);
retval=fread(iteration,sizeof(ts_uint),1,fh);
@@ -750,22 +752,6 @@
}
-ts_bool write_dout_fcompat_file(ts_vesicle *vesicle, ts_char *filename){
- FILE *fh;
- fh=fopen(filename, "w");
- if(fh==NULL){
- err("Cannot open file %s for writing");
- return TS_FAIL;
- }
- fprintf(fh,"%.17E\n%.17E\n",vesicle->stepsize,vesicle->dmax);
- fprint_vertex_list(fh,vesicle->vlist);
- fprint_tristar(fh,vesicle);
- fprint_triangle_list(fh,vesicle);
- fprint_vertex_data(fh,vesicle->vlist);
- fprint_bonds(fh,vesicle);
- fclose(fh);
- return TS_SUCCESS;
-}
ts_bool read_tape_fcompat_file(ts_vesicle *vesicle, ts_char *filename){
FILE *fh;
@@ -826,6 +812,7 @@
ts_bond_list *blist=vesicle->blist;
ts_vertex **vtx=vlist->vtx;
ts_uint i,j;
+ //ts_double senergy=0.0;
char filename[10000];
char just_name[255];
FILE *fh;
@@ -844,7 +831,8 @@
ts_uint monono=0, polyno=0, poly_idx=0, filno=0, fonono=0;
ts_bool poly=0, fil=0;
if(vesicle->poly_list!=NULL){
- if(vesicle->poly_list->poly[0]!=NULL){
+ if(vesicle->poly_list->n!=0){
+ //if(vesicle->poly_list->poly[0]!=NULL){
polyno=vesicle->poly_list->n;
monono=vesicle->poly_list->poly[0]->vlist->n;
poly=1;
@@ -852,7 +840,8 @@
}
if(vesicle->filament_list!=NULL){
- if(vesicle->filament_list->poly[0]!=NULL){
+ if(vesicle->filament_list->n!=0){
+ //if(vesicle->filament_list->poly[0]!=NULL){
filno=vesicle->filament_list->n;
fonono=vesicle->filament_list->poly[0]->vlist->n;
fil=1;
@@ -947,6 +936,30 @@
}
}
fprintf(fh,"</DataArray>\n");
+ fprintf(fh,"<DataArray type=\"Float64\" Name=\"direct_interaction_force\" format=\"ascii\">");
+ for(i=0;i<vlist->n;i++){
+ fprintf(fh,"%.17e ",vtx[i]->direct_interaction_force);
+ }
+ //polymeres
+ if(poly){
+ poly_idx=vlist->n;
+ for(i=0;i<vesicle->poly_list->n;i++){
+ for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++,poly_idx++){
+ fprintf(fh,"%.17e ", vesicle->poly_list->poly[i]->vlist->vtx[j]->direct_interaction_force);
+ }
+ }
+ }
+ //filaments
+ if(fil){
+ poly_idx=vlist->n+monono*polyno;
+ for(i=0;i<vesicle->filament_list->n;i++){
+ for(j=0;j<vesicle->filament_list->poly[i]->vlist->n;j++,poly_idx++){
+ // fprintf(stderr,"was here\n");
+ fprintf(fh,"%.17e ", vesicle->filament_list->poly[i]->vlist->vtx[j]->direct_interaction_force);
+ }
+ }
+ }
+ fprintf(fh,"</DataArray>\n");
//here comes additional data. Energy!
fprintf(fh,"<DataArray type=\"Float64\" Name=\"bending_energy\" format=\"ascii\">");
@@ -974,9 +987,26 @@
}
fprintf(fh,"</DataArray>\n");
-
- fprintf(fh,"</PointData>\n<CellData>\n</CellData>\n<Points>\n<DataArray type=\"Float64\" Name=\"Koordinate tock\" NumberOfComponents=\"3\" format=\"ascii\">\n");
+ fprintf(fh,"</PointData>\n<CellData>\n");
+
+ if(vesicle->tape->stretchswitch==1){
+ fprintf(fh,"<DataArray type=\"Float64\" Name=\"stretching_energy\" format=\"ascii\">");
+ for(i=0;i<blist->n;i++){
+ fprintf(fh, "0.0 ");
+ }
+ for(i=0;i<monono*polyno+filno*(fonono-1);i++){
+ fprintf(fh,"0.0 ");
+ }
+ for(i=0;i<vesicle->tlist->n;i++){
+ fprintf(fh,"%.17e ",vesicle->tlist->tria[i]->energy);
+ }
+ fprintf(fh,"</DataArray>\n");
+ }
+
+
+
+ fprintf(fh,"</CellData>\n<Points>\n<DataArray type=\"Float64\" Name=\"Koordinate tock\" NumberOfComponents=\"3\" format=\"ascii\">\n");
for(i=0;i<vlist->n;i++){
fprintf(fh,"%.17e %.17e %.17e\n",vtx[i]->x,vtx[i]->y, vtx[i]->z);
}
@@ -1165,6 +1195,8 @@
CFG_SIMPLE_INT("constvolswitch",&tape->constvolswitch),
CFG_SIMPLE_INT("constareaswitch",&tape->constareaswitch),
CFG_SIMPLE_FLOAT("constvolprecision",&tape->constvolprecision),
+ CFG_SIMPLE_INT("stretchswitch",&tape->stretchswitch),
+ CFG_SIMPLE_FLOAT("xkA0",&tape->xkA0),
CFG_SIMPLE_FLOAT("pressure",&tape->pressure),
CFG_SIMPLE_FLOAT("k_spring",&tape->kspring),
CFG_SIMPLE_FLOAT("xi",&tape->xi),
@@ -1185,12 +1217,23 @@
CFG_SIMPLE_FLOAT("c0",&tape->c0),
CFG_SIMPLE_FLOAT("w",&tape->w),
CFG_SIMPLE_FLOAT("F",&tape->F),
+/* Variables related to plane confinement */
+ CFG_INT("plane_confinement_switch", 0, CFGF_NONE),
+ CFG_FLOAT("plane_d", 15, CFGF_NONE),
+ CFG_FLOAT("plane_F", 1000, CFGF_NONE),
+/* Variables related to stretching */
+// CFG_FLOAT("stretchswitch", 0, CFGF_NONE),
+// CFG_FLOAT("xkA0",0,CFGF_NONE),
CFG_END()
};
cfg_t *cfg;
ts_uint retval;
cfg = cfg_init(opts, 0);
retval=cfg_parse_buf(cfg, buffer);
+ tape->plane_confinement_switch=cfg_getint(cfg,"plane_confinement_switch");
+ tape->plane_d=cfg_getfloat(cfg,"plane_d");
+ tape->plane_F=cfg_getfloat(cfg,"plane_F");
+
if(retval==CFG_FILE_ERROR){
fatal("No tape file.",100);
}
@@ -1219,6 +1262,8 @@
ts_bool getcmdline_tape(cfg_t *cfg, char *opts){
char *commands, *backup, *saveptr, *saveopptr, *command, *operator[2];
+ operator[0]=0;
+ operator[1]=0;
ts_uint i,j;
commands=(char *)malloc(10000*sizeof(char));
backup=commands; //since the pointer to commands will be lost, we acquire a pointer that will serve as backup.
--
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