tape fixed, output has additional timestamp, ncurrent iteration is dumped a...

Samo Penic

2014-03-08 1ab449a2d9d4433794736566014f5c311d5a9317

tape fixed, output has additional timestamp, ncurrent iteration is dumped and reread, but simulation is not restarted at correct time

 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);
    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;

 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 */


 src/initial_distribution.c

@@ -9,18 +9,15 @@
#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 = 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);
@@ -30,12 +27,42 @@
    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");
    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);

 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
 *

 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;
@@ -132,13 +132,14 @@

    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);

            
    /* global variables are set automatically */
    quiet=tape->quiet;
    return tape;
}

    return vesicle;

ts_bool tape_free(ts_tape *tape){
    free(tape->multiprocessing);
    free(tape);
    return TS_SUCCESS;
}



 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

 src/main.c

@@ -19,74 +19,30 @@
*/

int main(int argv, char *argc[]){
ts_uint inititer,mcsweeps, iterations;
ts_vesicle *vesicle, *vesicle1;


    ts_vesicle *vesicle;
    ts_tape *tape;
    ts_uint start_iteration=0;
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_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.
} 

 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

 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);
        }