From 1ab449a2d9d4433794736566014f5c311d5a9317 Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@gmail.com>
Date: Sat, 08 Mar 2014 16:33:08 +0000
Subject: [PATCH] tape fixed, output has additional timestamp, ncurrent iteration is dumped and reread, but simulation is not restarted at correct time
---
src/main.c | 66 ++-----------
src/timestep.c | 2
src/initial_distribution.h | 1
src/io.c | 95 ++++++++-----------
src/tape | 4
src/initial_distribution.c | 63 +++++++++---
src/general.h | 23 ++++
src/general.c | 14 ++
src/io.h | 7
9 files changed, 138 insertions(+), 137 deletions(-)
diff --git a/src/general.c b/src/general.c
index ed06398..a600800 100644
--- a/src/general.c
+++ b/src/general.c
@@ -3,10 +3,20 @@
#include "general.h"
#include<stdarg.h>
+#include <sys/time.h>
+#include <unistd.h>
+#include <time.h>
+
+
ts_uint ts_fprintf(FILE *fd, char *fmt, ...){
if(quiet) return TS_SUCCESS;
- va_list ap;
- va_start(ap,fmt);
+ va_list ap;
+ va_start(ap,fmt);
+ char tmbuf[255];
+ struct timeval now;
+ gettimeofday(&now, 0);
+ strftime(tmbuf, sizeof tmbuf, "%Y-%m-%d %H:%M:%S", localtime(&now.tv_sec));
+fprintf(fd, "[%s] ",tmbuf);
vfprintf(fd, fmt, ap); /* Call vfprintf */
va_end(ap); /* Cleanup the va_list */
return TS_SUCCESS;
diff --git a/src/general.h b/src/general.h
index 2999090..8da1878 100644
--- a/src/general.h
+++ b/src/general.h
@@ -3,7 +3,6 @@
#include<stdarg.h>
#include<stdio.h>
-
/* @brief This is a header file, defining general constants and structures.
* @file header.h
* @author Samo Penic
@@ -266,6 +265,28 @@
+typedef struct {
+ long int nshell;
+ long int ncxmax;
+ long int ncymax;
+ long int nczmax;
+ long int npoly;
+ long int nmono;
+ long int pswitch;
+ char *multiprocessing;
+ long int brezveze0;
+ long int brezveze1;
+ long int brezveze2;
+ ts_double xk0;
+ ts_double dmax;
+ ts_double stepsize;
+ ts_double kspring;
+ ts_double pressure;
+ long int iterations;
+ long int inititer;
+ long int mcsweeps;
+ long int quiet;
+} ts_tape;
/* GLOBAL VARIABLES */
diff --git a/src/initial_distribution.c b/src/initial_distribution.c
index b8f5965..4d5f565 100644
--- a/src/initial_distribution.c
+++ b/src/initial_distribution.c
@@ -9,33 +9,60 @@
#include "triangle.h"
#include "initial_distribution.h"
#include "energy.h"
+#include "poly.h"
ts_vesicle *initial_distribution_dipyramid(ts_uint nshell, ts_uint ncmax1, ts_uint ncmax2, ts_uint ncmax3, ts_double stepsize){
- ts_fprintf(stderr,"Starting initial_distribution on vesicle with %u shells!...\n",nshell);
+ ts_fprintf(stdout,"Starting initial_distribution on vesicle with %u shells!...\n",nshell);
ts_bool retval;
- ts_uint no_vertices=5*nshell*nshell+2;
-
-
-
- ts_vesicle *vesicle=init_vesicle(no_vertices,ncmax1,ncmax2,ncmax3,stepsize);
-
- vesicle->nshell=nshell;
- retval = vtx_set_global_values(vesicle);
- retval = pentagonal_dipyramid_vertex_distribution(vesicle->vlist);
- retval = init_vertex_neighbours(vesicle->vlist);
- vesicle->vlist = init_sort_neighbours(vesicle->blist,vesicle->vlist);
+ ts_uint no_vertices=5*nshell*nshell+2;
+ ts_vesicle *vesicle=init_vesicle(no_vertices,ncmax1,ncmax2,ncmax3,stepsize);
+ vesicle->nshell=nshell;
+ //retval = vtx_set_global_values(vesicle);
+ retval = pentagonal_dipyramid_vertex_distribution(vesicle->vlist);
+ retval = init_vertex_neighbours(vesicle->vlist);
+ vesicle->vlist = init_sort_neighbours(vesicle->blist,vesicle->vlist);
// retval = init_vesicle_bonds(vesicle); // bonds are created in sort_neigh
- retval = init_triangles(vesicle);
- retval = init_triangle_neighbours(vesicle);
- retval = init_common_vertex_triangle_neighbours(vesicle);
- retval = init_normal_vectors(vesicle->tlist);
- retval = mean_curvature_and_energy(vesicle);
- ts_fprintf(stderr,"initial_distribution finished!\n");
+ retval = init_triangles(vesicle);
+ retval = init_triangle_neighbours(vesicle);
+ retval = init_common_vertex_triangle_neighbours(vesicle);
+ retval = init_normal_vectors(vesicle->tlist);
+ retval = mean_curvature_and_energy(vesicle);
+ ts_fprintf(stdout,"initial_distribution finished!\n");
if(retval);
return vesicle;
}
+
+ts_vesicle *create_vesicle_from_tape(ts_tape *tape){
+ ts_vesicle *vesicle;
+ vesicle=initial_distribution_dipyramid(tape->nshell,tape->ncxmax,tape->ncymax,tape->nczmax,tape->stepsize);
+ vesicle->poly_list=init_poly_list(tape->npoly,tape->nmono, vesicle->vlist);
+ vesicle->spring_constant=tape->kspring;
+ poly_assign_spring_const(vesicle);
+
+ vesicle->nshell=tape->nshell;
+ vesicle->dmax=tape->dmax*tape->dmax; /* dmax^2 in the vesicle dmax variable */
+ vesicle->bending_rigidity=tape->xk0;
+ vtx_set_global_values(vesicle); /* make xk0 default value for every vertex */
+ ts_fprintf(stdout, "Tape setting: xk0=%e\n",tape->xk0);
+ vesicle->stepsize=tape->stepsize;
+ vesicle->clist->ncmax[0]=tape->ncxmax;
+ vesicle->clist->ncmax[1]=tape->ncymax;
+ vesicle->clist->ncmax[2]=tape->nczmax;
+ vesicle->clist->max_occupancy=8; /* hard coded max occupancy? */
+
+ vesicle->pressure= tape->pressure;
+ vesicle->pswitch=tape->pswitch;
+
+ return vesicle;
+
+}
+
+
+
+
+
ts_bool pentagonal_dipyramid_vertex_distribution(ts_vertex_list *vlist){
/* Some often used relations */
const ts_double s1= sin(2.0*M_PI/5.0);
diff --git a/src/initial_distribution.h b/src/initial_distribution.h
index 7b3e2ba..ef07da9 100644
--- a/src/initial_distribution.h
+++ b/src/initial_distribution.h
@@ -10,6 +10,7 @@
*/
ts_vesicle *initial_distribution_dipyramid(ts_uint nshell, ts_uint ncmax1, ts_uint ncmax2, ts_uint ncmax3, ts_double stepsize);
+ts_vesicle *create_vesicle_from_tape(ts_tape *tape);
/** Sets the initial position of the vertexes to dipyramid
*
diff --git a/src/io.c b/src/io.c
index 93fda4c..d1a2e3e 100644
--- a/src/io.c
+++ b/src/io.c
@@ -18,7 +18,7 @@
#include <errno.h>
/** DUMP STATE TO DISK DRIVE **/
-ts_bool dump_state(ts_vesicle *vesicle){
+ts_bool dump_state(ts_vesicle *vesicle, ts_uint iteration){
/* save current state with wrong pointers. Will fix that later */
ts_uint i,j,k;
@@ -131,14 +131,15 @@
*/
fwrite(vesicle->clist, sizeof(ts_cell_list),1, fh);
-
+
+ fwrite(&iteration, sizeof(ts_uint),1,fh);
fclose(fh);
return TS_SUCCESS;
}
/** RESTORE DUMP FROM DISK **/
-ts_vesicle *restore_state(){
+ts_vesicle *restore_state(ts_uint *iteration){
ts_uint i,j,k;
FILE *fh=fopen("dump.bin","rb");
ts_uint retval;
@@ -316,6 +317,7 @@
vesicle->clist->cell[i]->idx=i+1; // We enumerate cells! Probably never required!
}
+ retval=fread(iteration,sizeof(ts_uint),1,fh);
if(retval);
fclose(fh);
return vesicle;
@@ -750,80 +752,63 @@
-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, pswitch=0; // THIS IS DUE TO CONFUSE BUG!
- char *buf=malloc(255*sizeof(char));
- long int brezveze0=1;
+ts_tape *parsetape(char *filename){
+ // long int nshell=17,ncxmax=60, ncymax=60, nczmax=60, npoly=10, nmono=20, pswitch=0; // THIS IS DUE TO CONFUSE BUG!
+ ts_tape *tape=(ts_tape *)calloc(1,sizeof(ts_tape));
+ tape->multiprocessing=calloc(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,pressure=0.0;
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_INT("pswitch",&pswitch),
- CFG_SIMPLE_FLOAT("pressure",&pressure),
- 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",&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_SIMPLE_INT("nshell", &tape->nshell),
+ CFG_SIMPLE_INT("npoly", &tape->npoly),
+ CFG_SIMPLE_INT("nmono", &tape->nmono),
+ CFG_SIMPLE_FLOAT("dmax", &tape->dmax),
+ CFG_SIMPLE_FLOAT("xk0",&tape->xk0),
+ CFG_SIMPLE_INT("pswitch",&tape->pswitch),
+ CFG_SIMPLE_FLOAT("pressure",&tape->pressure),
+ CFG_SIMPLE_FLOAT("k_spring",&tape->kspring),
+ CFG_SIMPLE_FLOAT("stepsize",&tape->stepsize),
+ CFG_SIMPLE_INT("nxmax", &tape->ncxmax),
+ CFG_SIMPLE_INT("nymax", &tape->ncymax),
+ CFG_SIMPLE_INT("nzmax", &tape->nczmax),
+ CFG_SIMPLE_INT("iterations",&tape->iterations),
+ CFG_SIMPLE_INT("mcsweeps",&tape->mcsweeps),
+ CFG_SIMPLE_INT("inititer", &tape->inititer),
+ CFG_SIMPLE_BOOL("quiet",&tape->quiet),
+ CFG_SIMPLE_STR("multiprocessing",tape->multiprocessing),
+ CFG_SIMPLE_INT("smp_cores",&tape->brezveze0),
+ CFG_SIMPLE_INT("cluster_nodes",&tape->brezveze1),
+ CFG_SIMPLE_INT("distributed_processes",&tape->brezveze2),
CFG_END()
};
cfg_t *cfg;
ts_uint retval;
cfg = cfg_init(opts, 0);
- retval=cfg_parse(cfg, "tape");
+ retval=cfg_parse(cfg, filename);
if(retval==CFG_FILE_ERROR){
fatal("No tape file.",100);
}
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;
- vtx_set_global_values(vesicle); //copies xk0 to every vertex
-
-
- vesicle->stepsize=stepsize;
- vesicle->clist->ncmax[0]=ncxmax;
- vesicle->clist->ncmax[1]=ncymax;
- vesicle->clist->ncmax[2]=nczmax;
- vesicle->clist->max_occupancy=8;
- vesicle->pressure=pressure/vesicle->bending_rigidity; //all energy contributions need to be divided by bending_rigidity!
- vesicle->pswitch=pswitch;
cfg_free(cfg);
- free(buf);
- // fprintf(stderr,"NSHELL=%u\n",vesicle->nshell);
-
- return vesicle;
+ /* global variables are set automatically */
+ quiet=tape->quiet;
+ return tape;
+}
+ts_bool tape_free(ts_tape *tape){
+ free(tape->multiprocessing);
+ free(tape);
+ return TS_SUCCESS;
}
diff --git a/src/io.h b/src/io.h
index f76eb09..8f14b68 100644
--- a/src/io.h
+++ b/src/io.h
@@ -60,8 +60,9 @@
ts_bool write_vertex_vtk_file(ts_vesicle *vesicle,ts_char *filename, ts_char *text);
ts_bool write_vertex_xml_file(ts_vesicle *vesicle, ts_uint timestepno);
ts_bool write_master_xml_file(ts_char *filename);
-ts_vesicle *parsetape(ts_uint *mcsweeps, ts_uint *inititer, ts_uint *iterations);
+ts_tape *parsetape(char *filename);
+ts_bool tape_free(ts_tape *tape);
-ts_bool dump_state(ts_vesicle *vesicle);
-ts_vesicle *restore_state();
+ts_bool dump_state(ts_vesicle *vesicle, ts_uint iteration);
+ts_vesicle *restore_state(ts_uint *iteration);
#endif
diff --git a/src/main.c b/src/main.c
index 0c955dc..44d90e2 100644
--- a/src/main.c
+++ b/src/main.c
@@ -19,74 +19,30 @@
*/
int main(int argv, char *argc[]){
-ts_uint inititer,mcsweeps, iterations;
-ts_vesicle *vesicle, *vesicle1;
-
-
-parse_args(argv,argc);
-
-/* THIS SHOULD GO INTO UNIT TEST
-ts_bool retval;
- ts_vertex_list *vlist=init_vertex_list(5);
-ts_vertex_list *vlist1;
-ts_bond_list *blist=init_bond_list();
-ts_triangle_list *tlist=init_triangle_list();
-ts_cell_list *clist=init_cell_list(3,3,3,0.3);
-
-retval=vtx_add_cneighbour(blist,vlist->vtx[1],vlist->vtx[0]);
-if(retval==TS_FAIL) printf("1. already a member or vertex is null!\n");
-
-retval=vtx_add_neighbour(vlist->vtx[0],vlist->vtx[1]);
-if(retval==TS_FAIL) printf("2. already a member or vertex is null!\n");
-fprintf(stderr,"Was here");
-retval=vtx_remove_neighbour(vlist->vtx[1],vlist->vtx[0]);
-vtx_add_neighbour(vlist->vtx[0],vlist->vtx[1]);
-fprintf(stderr,"Was here too!\n");
-
-vlist->vtx[0]->x=1.0;
-vlist->vtx[0]->x=1.1;
-vlist1=vertex_list_copy(vlist);
-bond_add(blist, vlist->vtx[1],vlist->vtx[0]);
-triangle_add(tlist,vlist->vtx[1],vlist->vtx[2],vlist->vtx[3]);
-
-triangle_add(tlist,vlist->vtx[1],vlist->vtx[2],vlist->vtx[3]);
-
-printf("Cell idx=1 has vertices=%u\n",clist->cell[0]->nvertex);
-cell_add_vertex(clist->cell[0], vlist->vtx[0]);
-printf("Cell idx=1 has vertices=%u\n",clist->cell[0]->nvertex);
-printf("Cell idx=1 has vertex[0] has x coordinate=%e\n",clist->cell[0]->vertex[0]->x);
-cell_list_cell_occupation_clear(clist);
-printf("Cell idx=1 has vertices=%u\n",clist->cell[0]->nvertex);
-cell_add_vertex(clist->cell[0], vlist->vtx[0]);
-
-
-triangle_list_free(tlist);
-bond_list_free(blist);
-vtx_list_free(vlist);
-cell_list_free(clist);
-
-vtx_list_free(vlist1);
-printf("Tests complete.\n");
-*/
+ ts_vesicle *vesicle;
+ ts_tape *tape;
+ ts_uint start_iteration=0;
+ parse_args(argv,argc);
+ ts_fprintf(stdout,"\nStarting program...\n\n");
if(force_from_tape){
ts_fprintf(stdout,"****************************************************\n");
ts_fprintf(stdout,"**** Reinitializing initial geometry from tape *****\n");
ts_fprintf(stdout,"****************************************************\n\n");
-vesicle=parsetape(&mcsweeps, &inititer, &iterations);
+tape=parsetape("tape");
+vesicle=create_vesicle_from_tape(tape);
} else {
ts_fprintf(stdout,"**********************************************************************\n");
ts_fprintf(stdout,"**** Recreating vesicle from dump file and continuing simulation *****\n");
ts_fprintf(stdout,"**********************************************************************\n\n");
-vesicle1=parsetape(&mcsweeps, &inititer, &iterations);
-vesicle=restore_state();
-vesicle_free(vesicle1);
+tape=parsetape("tape");
+vesicle=restore_state(&start_iteration);
}
-run_simulation(vesicle, mcsweeps, inititer, iterations);
+run_simulation(vesicle, tape->mcsweeps, tape->inititer, tape->iterations);
write_master_xml_file("test.pvd");
write_dout_fcompat_file(vesicle,"dout");
vesicle_free(vesicle);
-
+tape_free(tape);
return 0; //program finished perfectly ok. We return 0.
}
diff --git a/src/tape b/src/tape
index 18eea15..59b417a 100644
--- a/src/tape
+++ b/src/tape
@@ -4,7 +4,7 @@
# dmax is the max. bond length (in units l_min)
dmax=1.7
# bending rigidity of the membrane (in units kT)
-xk0=1.0
+xk0=25.0
# max step size (in units l_min)
stepsize=0.15
@@ -16,7 +16,7 @@
####### Polymer definitions ###########
# npoly is a number of polymers attached to npoly distinct vertices on vesicle
-npoly=0
+npoly=20
# nmono is a number of monomers in each polymer
nmono=10
# Spring constant between monomers of the polymer
diff --git a/src/timestep.c b/src/timestep.c
index 8ae5a30..4ac20be 100644
--- a/src/timestep.c
+++ b/src/timestep.c
@@ -22,7 +22,7 @@
centermass(vesicle);
cell_occupation(vesicle);
ts_fprintf(stdout,"Done %d out of %d iterations (x %d MC sweeps).\n",i+1,inititer+iterations,mcsweeps);
- dump_state(vesicle);
+ dump_state(vesicle,i);
if(i>inititer){
write_vertex_xml_file(vesicle,i-inititer);
}
--
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