#include <sys/stat.h>
#include <fcntl.h>
#include <unistd.h>
+#include <sys/time.h>
+#include <time.h>
#include <math.h>
#include "moldyn.h"
+#include "report/report.h"
-#include "math/math.h"
-#include "init/init.h"
-#include "random/random.h"
-#include "visual/visual.h"
-#include "list/list.h"
+/* potential includes */
+#include "potentials/harmonic_oscillator.h"
+#include "potentials/lennard_jones.h"
+#include "potentials/albe.h"
+#ifdef TERSOFF_ORIG
+#include "potentials/tersoff_orig.h"
+#else
+#include "potentials/tersoff.h"
+#endif
-int moldyn_init(t_moldyn *moldyn,int argc,char **argv) {
+/*
+ * global variables, pse and atom colors (only needed here)
+ */
+
+static char *pse_name[]={
+ "*",
+ "H",
+ "He",
+ "Li",
+ "Be",
+ "B",
+ "C",
+ "N",
+ "O",
+ "F",
+ "Ne",
+ "Na",
+ "Mg",
+ "Al",
+ "Si",
+ "P",
+ "S",
+ "Cl",
+ "Ar",
+};
+
+static char *pse_col[]={
+ "*",
+ "White",
+ "He",
+ "Li",
+ "Be",
+ "B",
+ "Gray",
+ "N",
+ "Blue",
+ "F",
+ "Ne",
+ "Na",
+ "Mg",
+ "Al",
+ "Yellow",
+ "P",
+ "S",
+ "Cl",
+ "Ar",
+};
+
+/*
+ * the moldyn functions
+ */
- //int ret;
+int moldyn_init(t_moldyn *moldyn,int argc,char **argv) {
- //ret=moldyn_parse_argv(moldyn,argc,argv);
- //if(ret<0) return ret;
+ printf("[moldyn] init\n");
memset(moldyn,0,sizeof(t_moldyn));
+ moldyn->argc=argc;
+ moldyn->args=argv;
+
rand_init(&(moldyn->random),NULL,1);
moldyn->random.status|=RAND_STAT_VERBOSE;
int moldyn_shutdown(t_moldyn *moldyn) {
printf("[moldyn] shutdown\n");
+
moldyn_log_shutdown(moldyn);
link_cell_shutdown(moldyn);
rand_close(&(moldyn->random));
int set_int_alg(t_moldyn *moldyn,u8 algo) {
+ printf("[moldyn] integration algorithm: ");
+
switch(algo) {
case MOLDYN_INTEGRATE_VERLET:
moldyn->integrate=velocity_verlet;
+ printf("velocity verlet\n");
break;
default:
printf("unknown integration algorithm: %02x\n",algo);
+ printf("unknown\n");
return -1;
}
moldyn->cutoff=cutoff;
+ printf("[moldyn] cutoff [A]: %f\n",moldyn->cutoff);
+
+ return 0;
+}
+
+int set_bondlen(t_moldyn *moldyn,double b0,double b1,double bm) {
+
+ moldyn->bondlen[0]=b0*b0;
+ moldyn->bondlen[1]=b1*b1;
+ if(bm<0)
+ moldyn->bondlen[2]=b0*b1;
+ else
+ moldyn->bondlen[2]=bm*bm;
+
return 0;
}
moldyn->t_ref=t_ref;
+ printf("[moldyn] temperature [K]: %f\n",moldyn->t_ref);
+
+ return 0;
+}
+
+int set_pressure(t_moldyn *moldyn,double p_ref) {
+
+ moldyn->p_ref=p_ref;
+
+ printf("[moldyn] pressure [bar]: %f\n",moldyn->p_ref/BAR);
+
return 0;
}
moldyn->t_tc=ttc;
moldyn->p_tc=ptc;
+ printf("[moldyn] p/t scaling:\n");
+
+ printf(" p: %s",ptype?"yes":"no ");
+ if(ptype)
+ printf(" | type: %02x | factor: %f",ptype,ptc);
+ printf("\n");
+
+ printf(" t: %s",ttype?"yes":"no ");
+ if(ttype)
+ printf(" | type: %02x | factor: %f",ttype,ttc);
+ printf("\n");
+
return 0;
}
moldyn->dim.y=y;
moldyn->dim.z=z;
+ moldyn->volume=x*y*z;
+
if(visualize) {
moldyn->vis.dim.x=x;
moldyn->vis.dim.y=y;
moldyn->vis.dim.z=z;
}
+ printf("[moldyn] dimensions in A and A^3 respectively:\n");
+ printf(" x: %f\n",moldyn->dim.x);
+ printf(" y: %f\n",moldyn->dim.y);
+ printf(" z: %f\n",moldyn->dim.z);
+ printf(" volume: %f\n",moldyn->volume);
+ printf(" visualize simulation box: %s\n",visualize?"yes":"no");
+
return 0;
}
int set_pbc(t_moldyn *moldyn,u8 x,u8 y,u8 z) {
+ printf("[moldyn] periodic boundary conditions:\n");
+
if(x)
moldyn->status|=MOLDYN_STAT_PBX;
if(z)
moldyn->status|=MOLDYN_STAT_PBZ;
+ printf(" x: %s\n",x?"yes":"no");
+ printf(" y: %s\n",y?"yes":"no");
+ printf(" z: %s\n",z?"yes":"no");
+
return 0;
}
-int set_potential1b(t_moldyn *moldyn,pf_func1b func,void *params) {
+int set_potential(t_moldyn *moldyn,u8 type) {
- moldyn->func1b=func;
- moldyn->pot1b_params=params;
+ switch(type) {
+ case MOLDYN_POTENTIAL_TM:
+ moldyn->func1b=tersoff_mult_1bp;
+ moldyn->func3b_j1=tersoff_mult_3bp_j1;
+ moldyn->func3b_k1=tersoff_mult_3bp_k1;
+ moldyn->func3b_j2=tersoff_mult_3bp_j2;
+ moldyn->func3b_k2=tersoff_mult_3bp_k2;
+ // missing: check 2b bond func
+ break;
+ case MOLDYN_POTENTIAL_AM:
+ moldyn->func3b_j1=albe_mult_3bp_j1;
+ moldyn->func3b_k1=albe_mult_3bp_k1;
+ moldyn->func3b_j2=albe_mult_3bp_j2;
+ moldyn->func3b_k2=albe_mult_3bp_k2;
+ moldyn->check_2b_bond=albe_mult_check_2b_bond;
+ break;
+ case MOLDYN_POTENTIAL_HO:
+ moldyn->func2b=harmonic_oscillator;
+ moldyn->check_2b_bond=harmonic_oscillator_check_2b_bond;
+ break;
+ case MOLDYN_POTENTIAL_LJ:
+ moldyn->func2b=lennard_jones;
+ moldyn->check_2b_bond=lennard_jones_check_2b_bond;
+ break;
+ default:
+ printf("[moldyn] set potential: unknown type %02x\n",
+ type);
+ return -1;
+ }
return 0;
}
-int set_potential2b(t_moldyn *moldyn,pf_func2b func,void *params) {
+int set_avg_skip(t_moldyn *moldyn,int skip) {
- moldyn->func2b=func;
- moldyn->pot2b_params=params;
+ printf("[moldyn] skip %d steps before starting average calc\n",skip);
+ moldyn->avg_skip=skip;
return 0;
}
-int set_potential2b_post(t_moldyn *moldyn,pf_func2b_post func,void *params) {
+int moldyn_set_log_dir(t_moldyn *moldyn,char *dir) {
- moldyn->func2b=func;
- moldyn->pot2b_params=params;
+ strncpy(moldyn->vlsdir,dir,127);
return 0;
}
-int set_potential3b(t_moldyn *moldyn,pf_func3b func,void *params) {
+int moldyn_set_report(t_moldyn *moldyn,char *author,char *title) {
- moldyn->func3b=func;
- moldyn->pot3b_params=params;
+ strncpy(moldyn->rauthor,author,63);
+ strncpy(moldyn->rtitle,title,63);
return 0;
}
+
+int moldyn_set_log(t_moldyn *moldyn,u8 type,int timer) {
+
+ char filename[128];
+ int ret;
-int moldyn_set_log(t_moldyn *moldyn,u8 type,char *fb,int timer) {
+ printf("[moldyn] set log: ");
switch(type) {
case LOG_TOTAL_ENERGY:
moldyn->ewrite=timer;
- moldyn->efd=open(fb,O_WRONLY|O_CREAT|O_TRUNC);
+ snprintf(filename,127,"%s/energy",moldyn->vlsdir);
+ moldyn->efd=open(filename,
+ O_WRONLY|O_CREAT|O_EXCL,
+ S_IRUSR|S_IWUSR);
if(moldyn->efd<0) {
- perror("[moldyn] efd open");
+ perror("[moldyn] energy log fd open");
return moldyn->efd;
}
dprintf(moldyn->efd,"# total energy log file\n");
+ printf("total energy (%d)\n",timer);
break;
case LOG_TOTAL_MOMENTUM:
moldyn->mwrite=timer;
- moldyn->mfd=open(fb,O_WRONLY|O_CREAT|O_TRUNC);
+ snprintf(filename,127,"%s/momentum",moldyn->vlsdir);
+ moldyn->mfd=open(filename,
+ O_WRONLY|O_CREAT|O_EXCL,
+ S_IRUSR|S_IWUSR);
if(moldyn->mfd<0) {
- perror("[moldyn] mfd open");
+ perror("[moldyn] momentum log fd open");
return moldyn->mfd;
}
dprintf(moldyn->efd,"# total momentum log file\n");
+ printf("total momentum (%d)\n",timer);
+ break;
+ case LOG_PRESSURE:
+ moldyn->pwrite=timer;
+ snprintf(filename,127,"%s/pressure",moldyn->vlsdir);
+ moldyn->pfd=open(filename,
+ O_WRONLY|O_CREAT|O_EXCL,
+ S_IRUSR|S_IWUSR);
+ if(moldyn->pfd<0) {
+ perror("[moldyn] pressure log file\n");
+ return moldyn->pfd;
+ }
+ dprintf(moldyn->pfd,"# pressure log file\n");
+ printf("pressure (%d)\n",timer);
+ break;
+ case LOG_TEMPERATURE:
+ moldyn->twrite=timer;
+ snprintf(filename,127,"%s/temperature",moldyn->vlsdir);
+ moldyn->tfd=open(filename,
+ O_WRONLY|O_CREAT|O_EXCL,
+ S_IRUSR|S_IWUSR);
+ if(moldyn->tfd<0) {
+ perror("[moldyn] temperature log file\n");
+ return moldyn->tfd;
+ }
+ dprintf(moldyn->tfd,"# temperature log file\n");
+ printf("temperature (%d)\n",timer);
+ break;
+ case LOG_VOLUME:
+ moldyn->vwrite=timer;
+ snprintf(filename,127,"%s/volume",moldyn->vlsdir);
+ moldyn->vfd=open(filename,
+ O_WRONLY|O_CREAT|O_EXCL,
+ S_IRUSR|S_IWUSR);
+ if(moldyn->vfd<0) {
+ perror("[moldyn] volume log file\n");
+ return moldyn->vfd;
+ }
+ dprintf(moldyn->vfd,"# volume log file\n");
+ printf("volume (%d)\n",timer);
break;
case SAVE_STEP:
moldyn->swrite=timer;
- strncpy(moldyn->sfb,fb,63);
+ printf("save file (%d)\n",timer);
break;
case VISUAL_STEP:
- moldyn->vwrite=timer;
- strncpy(moldyn->vfb,fb,63);
- visual_init(&(moldyn->vis),fb);
+ moldyn->awrite=timer;
+ ret=visual_init(moldyn,moldyn->vlsdir);
+ if(ret<0) {
+ printf("[moldyn] visual init failure\n");
+ return ret;
+ }
+ printf("visual file (%d)\n",timer);
+ break;
+ case CREATE_REPORT:
+ snprintf(filename,127,"%s/report.tex",moldyn->vlsdir);
+ moldyn->rfd=open(filename,
+ O_WRONLY|O_CREAT|O_EXCL,
+ S_IRUSR|S_IWUSR);
+ if(moldyn->rfd<0) {
+ perror("[moldyn] report fd open");
+ return moldyn->rfd;
+ }
+ printf("report -> ");
+ if(moldyn->efd) {
+ snprintf(filename,127,"%s/e_plot.scr",
+ moldyn->vlsdir);
+ moldyn->epfd=open(filename,
+ O_WRONLY|O_CREAT|O_EXCL,
+ S_IRUSR|S_IWUSR);
+ if(moldyn->epfd<0) {
+ perror("[moldyn] energy plot fd open");
+ return moldyn->epfd;
+ }
+ dprintf(moldyn->epfd,e_plot_script);
+ close(moldyn->epfd);
+ printf("energy ");
+ }
+ if(moldyn->pfd) {
+ snprintf(filename,127,"%s/pressure_plot.scr",
+ moldyn->vlsdir);
+ moldyn->ppfd=open(filename,
+ O_WRONLY|O_CREAT|O_EXCL,
+ S_IRUSR|S_IWUSR);
+ if(moldyn->ppfd<0) {
+ perror("[moldyn] p plot fd open");
+ return moldyn->ppfd;
+ }
+ dprintf(moldyn->ppfd,pressure_plot_script);
+ close(moldyn->ppfd);
+ printf("pressure ");
+ }
+ if(moldyn->tfd) {
+ snprintf(filename,127,"%s/temperature_plot.scr",
+ moldyn->vlsdir);
+ moldyn->tpfd=open(filename,
+ O_WRONLY|O_CREAT|O_EXCL,
+ S_IRUSR|S_IWUSR);
+ if(moldyn->tpfd<0) {
+ perror("[moldyn] t plot fd open");
+ return moldyn->tpfd;
+ }
+ dprintf(moldyn->tpfd,temperature_plot_script);
+ close(moldyn->tpfd);
+ printf("temperature ");
+ }
+ dprintf(moldyn->rfd,report_start,
+ moldyn->rauthor,moldyn->rtitle);
+ printf("\n");
break;
default:
- printf("unknown log mechanism: %02x\n",type);
+ printf("unknown log type: %02x\n",type);
return -1;
}
int moldyn_log_shutdown(t_moldyn *moldyn) {
+ char sc[256];
+
printf("[moldyn] log shutdown\n");
- if(moldyn->efd) close(moldyn->efd);
+ if(moldyn->efd) {
+ close(moldyn->efd);
+ if(moldyn->rfd) {
+ dprintf(moldyn->rfd,report_energy);
+ snprintf(sc,255,"cd %s && gnuplot e_plot.scr",
+ moldyn->vlsdir);
+ system(sc);
+ }
+ }
if(moldyn->mfd) close(moldyn->mfd);
- if(&(moldyn->vis)) visual_tini(&(moldyn->vis));
+ if(moldyn->pfd) {
+ close(moldyn->pfd);
+ if(moldyn->rfd)
+ dprintf(moldyn->rfd,report_pressure);
+ snprintf(sc,255,"cd %s && gnuplot pressure_plot.scr",
+ moldyn->vlsdir);
+ system(sc);
+ }
+ if(moldyn->tfd) {
+ close(moldyn->tfd);
+ if(moldyn->rfd)
+ dprintf(moldyn->rfd,report_temperature);
+ snprintf(sc,255,"cd %s && gnuplot temperature_plot.scr",
+ moldyn->vlsdir);
+ system(sc);
+ }
+ if(moldyn->rfd) {
+ dprintf(moldyn->rfd,report_end);
+ close(moldyn->rfd);
+ snprintf(sc,255,"cd %s && pdflatex report >/dev/null 2>&1",
+ moldyn->vlsdir);
+ system(sc);
+ snprintf(sc,255,"cd %s && pdflatex report >/dev/null 2>&1",
+ moldyn->vlsdir);
+ system(sc);
+ snprintf(sc,255,"cd %s && dvipdf report >/dev/null 2>&1",
+ moldyn->vlsdir);
+ system(sc);
+ }
return 0;
}
+/*
+ * creating lattice functions
+ */
+
int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass,
- u8 attr,u8 bnum,int a,int b,int c) {
+ u8 attr,u8 brand,int a,int b,int c,t_3dvec *origin) {
- int count;
+ int new,count;
int ret;
- t_3dvec origin;
-
- count=a*b*c;
+ t_3dvec orig;
+ void *ptr;
+ t_atom *atom;
- if(type==FCC) count*=4;
+ new=a*b*c;
+ count=moldyn->count;
- if(type==DIAMOND) count*=8;
+ /* how many atoms do we expect */
+ if(type==CUBIC) new*=1;
+ if(type==FCC) new*=4;
+ if(type==DIAMOND) new*=8;
- moldyn->atom=malloc(count*sizeof(t_atom));
- if(moldyn->atom==NULL) {
- perror("malloc (atoms)");
+ /* allocate space for atoms */
+ ptr=realloc(moldyn->atom,(count+new)*sizeof(t_atom));
+ if(!ptr) {
+ perror("[moldyn] realloc (create lattice)");
return -1;
}
+ moldyn->atom=ptr;
+ atom=&(moldyn->atom[count]);
- v3_zero(&origin);
+ /* no atoms on the boundaries (only reason: it looks better!) */
+ if(!origin) {
+ orig.x=0.5*lc;
+ orig.y=0.5*lc;
+ orig.z=0.5*lc;
+ }
+ else {
+ orig.x=origin->x;
+ orig.y=origin->y;
+ orig.z=origin->z;
+ }
switch(type) {
+ case CUBIC:
+ set_nn_dist(moldyn,lc);
+ ret=cubic_init(a,b,c,lc,atom,&orig);
+ break;
case FCC:
- ret=fcc_init(a,b,c,lc,moldyn->atom,&origin);
+ if(!origin)
+ v3_scale(&orig,&orig,0.5);
+ set_nn_dist(moldyn,0.5*sqrt(2.0)*lc);
+ ret=fcc_init(a,b,c,lc,atom,&orig);
break;
case DIAMOND:
- ret=diamond_init(a,b,c,lc,moldyn->atom,&origin);
+ if(!origin)
+ v3_scale(&orig,&orig,0.25);
+ set_nn_dist(moldyn,0.25*sqrt(3.0)*lc);
+ ret=diamond_init(a,b,c,lc,atom,&orig);
break;
default:
printf("unknown lattice type (%02x)\n",type);
}
/* debug */
- if(ret!=count) {
- printf("ok, there is something wrong ...\n");
- printf("calculated -> %d atoms\n",count);
- printf("created -> %d atoms\n",ret);
+ if(ret!=new) {
+ printf("[moldyn] creating lattice failed\n");
+ printf(" amount of atoms\n");
+ printf(" - expected: %d\n",new);
+ printf(" - created: %d\n",ret);
return -1;
}
- moldyn->count=count;
- printf("[moldyn] created lattice with %d atoms\n",count);
-
- while(count) {
- count-=1;
- moldyn->atom[count].element=element;
- moldyn->atom[count].mass=mass;
- moldyn->atom[count].attr=attr;
- moldyn->atom[count].bnum=bnum;
- check_per_bound(moldyn,&(moldyn->atom[count].r));
+ moldyn->count+=new;
+ printf("[moldyn] created lattice with %d atoms\n",new);
+
+ for(ret=0;ret<new;ret++) {
+ atom[ret].element=element;
+ atom[ret].mass=mass;
+ atom[ret].attr=attr;
+ atom[ret].brand=brand;
+ atom[ret].tag=count+ret;
+ check_per_bound(moldyn,&(atom[ret].r));
+ atom[ret].r_0=atom[ret].r;
}
+ /* update total system mass */
+ total_mass_calc(moldyn);
return ret;
}
-int add_atom(t_moldyn *moldyn,int element,double mass,u8 bnum,u8 attr,
+int add_atom(t_moldyn *moldyn,int element,double mass,u8 brand,u8 attr,
t_3dvec *r,t_3dvec *v) {
t_atom *atom;
int count;
atom=moldyn->atom;
- count=++(moldyn->count);
+ count=(moldyn->count)++; // asshole style!
- ptr=realloc(atom,count*sizeof(t_atom));
+ ptr=realloc(atom,(count+1)*sizeof(t_atom));
if(!ptr) {
perror("[moldyn] realloc (add atom)");
return -1;
moldyn->atom=ptr;
atom=moldyn->atom;
- atom[count-1].r=*r;
- atom[count-1].v=*v;
- atom[count-1].element=element;
- atom[count-1].mass=mass;
- atom[count-1].bnum=bnum;
- atom[count-1].attr=attr;
+
+ /* initialize new atom */
+ memset(&(atom[count]),0,sizeof(t_atom));
+ atom[count].r=*r;
+ atom[count].v=*v;
+ atom[count].element=element;
+ atom[count].mass=mass;
+ atom[count].brand=brand;
+ atom[count].tag=count;
+ atom[count].attr=attr;
+ check_per_bound(moldyn,&(atom[count].r));
+ atom[count].r_0=atom[count].r;
+
+ /* update total system mass */
+ total_mass_calc(moldyn);
+
+ return 0;
+}
+
+int del_atom(t_moldyn *moldyn,int tag) {
+
+ t_atom *new,*old;
+ int cnt;
+
+ old=moldyn->atom;
+
+ new=(t_atom *)malloc((moldyn->count-1)*sizeof(t_atom));
+ if(!new) {
+ perror("[moldyn]malloc (del atom)");
+ return -1;
+ }
+
+ for(cnt=0;cnt<tag;cnt++)
+ new[cnt]=old[cnt];
+
+ for(cnt=tag+1;cnt<moldyn->count;cnt++) {
+ new[cnt-1]=old[cnt];
+ new[cnt-1].tag=cnt-1;
+ }
+
+ moldyn->count-=1;
+ moldyn->atom=new;
+
+ free(old);
return 0;
}
+/* cubic init */
+int cubic_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin) {
+
+ int count;
+ t_3dvec r;
+ int i,j,k;
+ t_3dvec o;
+
+ count=0;
+ if(origin)
+ v3_copy(&o,origin);
+ else
+ v3_zero(&o);
+
+ r.x=o.x;
+ for(i=0;i<a;i++) {
+ r.y=o.y;
+ for(j=0;j<b;j++) {
+ r.z=o.z;
+ for(k=0;k<c;k++) {
+ v3_copy(&(atom[count].r),&r);
+ count+=1;
+ r.z+=lc;
+ }
+ r.y+=lc;
+ }
+ r.x+=lc;
+ }
+
+ for(i=0;i<count;i++) {
+ atom[i].r.x-=(a*lc)/2.0;
+ atom[i].r.y-=(b*lc)/2.0;
+ atom[i].r.z-=(c*lc)/2.0;
+ }
+
+ return count;
+}
+
+/* fcc lattice init */
+int fcc_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin) {
+
+ int count;
+ int i,j,k,l;
+ t_3dvec o,r,n;
+ t_3dvec basis[3];
+
+ count=0;
+ if(origin)
+ v3_copy(&o,origin);
+ else
+ v3_zero(&o);
+
+ /* construct the basis */
+ memset(basis,0,3*sizeof(t_3dvec));
+ basis[0].x=0.5*lc;
+ basis[0].y=0.5*lc;
+ basis[1].x=0.5*lc;
+ basis[1].z=0.5*lc;
+ basis[2].y=0.5*lc;
+ basis[2].z=0.5*lc;
+
+ /* fill up the room */
+ r.x=o.x;
+ for(i=0;i<a;i++) {
+ r.y=o.y;
+ for(j=0;j<b;j++) {
+ r.z=o.z;
+ for(k=0;k<c;k++) {
+ /* first atom */
+ v3_copy(&(atom[count].r),&r);
+ count+=1;
+ r.z+=lc;
+ /* the three face centered atoms */
+ for(l=0;l<3;l++) {
+ v3_add(&n,&r,&basis[l]);
+ v3_copy(&(atom[count].r),&n);
+ count+=1;
+ }
+ }
+ r.y+=lc;
+ }
+ r.x+=lc;
+ }
+
+ /* coordinate transformation */
+ for(i=0;i<count;i++) {
+ atom[i].r.x-=(a*lc)/2.0;
+ atom[i].r.y-=(b*lc)/2.0;
+ atom[i].r.z-=(c*lc)/2.0;
+ }
+
+ return count;
+}
+
+int diamond_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin) {
+
+ int count;
+ t_3dvec o;
+
+ count=fcc_init(a,b,c,lc,atom,origin);
+
+ o.x=0.25*lc;
+ o.y=0.25*lc;
+ o.z=0.25*lc;
+
+ if(origin) v3_add(&o,&o,origin);
+
+ count+=fcc_init(a,b,c,lc,&atom[count],&o);
+
+ return count;
+}
+
int destroy_atoms(t_moldyn *moldyn) {
if(moldyn->atom) free(moldyn->atom);
atom=moldyn->atom;
random=&(moldyn->random);
+ printf("[moldyn] thermal init (equi init: %s)\n",equi_init?"yes":"no");
+
/* gaussian distribution of velocities */
v3_zero(&p_total);
for(i=0;i<moldyn->count;i++) {
return 0;
}
+double total_mass_calc(t_moldyn *moldyn) {
+
+ int i;
+
+ moldyn->mass=0.0;
+
+ for(i=0;i<moldyn->count;i++)
+ moldyn->mass+=moldyn->atom[i].mass;
+
+ return moldyn->mass;
+}
+
+double temperature_calc(t_moldyn *moldyn) {
+
+ /* assume up to date kinetic energy, which is 3/2 N k_B T */
+
+ moldyn->t=(2.0*moldyn->ekin)/(3.0*K_BOLTZMANN*moldyn->count);
+
+ return moldyn->t;
+}
+
+double get_temperature(t_moldyn *moldyn) {
+
+ return moldyn->t;
+}
+
int scale_velocity(t_moldyn *moldyn,u8 equi_init) {
int i;
count=0;
for(i=0;i<moldyn->count;i++) {
if((equi_init&TRUE)||(atom[i].attr&ATOM_ATTR_HB)) {
- e+=0.5*atom[i].mass*v3_absolute_square(&(atom[i].v));
+ e+=atom[i].mass*v3_absolute_square(&(atom[i].v));
count+=1;
}
}
- if(count!=0) moldyn->t=(2.0*e)/(3.0*count*K_BOLTZMANN);
+ e*=0.5;
+ if(count!=0) moldyn->t=e/(1.5*count*K_BOLTZMANN);
else return 0; /* no atoms involved in scaling! */
/* (temporary) hack for e,t = 0 */
if(e==0.0) {
moldyn->t=0.0;
- if(moldyn->t_ref!=0.0)
+ if(moldyn->t_ref!=0.0) {
thermal_init(moldyn,equi_init);
+ return 0;
+ }
else
return 0; /* no scaling needed */
}
scale*=2.0;
else
if(moldyn->pt_scale&T_SCALE_BERENDSEN)
- scale=1.0+moldyn->tau*(scale-1.0)/moldyn->t_tc;
+ scale=1.0+(scale-1.0)/moldyn->t_tc;
scale=sqrt(scale);
/* velocity scaling */
- for(i=0;i<moldyn->count;i++)
+ for(i=0;i<moldyn->count;i++) {
if((equi_init&TRUE)||(atom[i].attr&ATOM_ATTR_HB))
v3_scale(&(atom[i].v),&(atom[i].v),scale);
+ }
return 0;
}
-double get_e_kin(t_moldyn *moldyn) {
-
- int i;
- t_atom *atom;
+double ideal_gas_law_pressure(t_moldyn *moldyn) {
- atom=moldyn->atom;
- moldyn->ekin=0.0;
+ double p;
- for(i=0;i<moldyn->count;i++)
- moldyn->ekin+=0.5*atom[i].mass*v3_absolute_square(&(atom[i].v));
+ p=moldyn->count*moldyn->t*K_BOLTZMANN/moldyn->volume;
- return moldyn->ekin;
+ return p;
}
-double get_e_pot(t_moldyn *moldyn) {
+double virial_sum(t_moldyn *moldyn) {
- return moldyn->energy;
-}
+ int i;
+ t_virial *virial;
+
+ /* virial (sum over atom virials) */
+ moldyn->virial=0.0;
+ moldyn->vir.xx=0.0;
+ moldyn->vir.yy=0.0;
+ moldyn->vir.zz=0.0;
+ moldyn->vir.xy=0.0;
+ moldyn->vir.xz=0.0;
+ moldyn->vir.yz=0.0;
+ for(i=0;i<moldyn->count;i++) {
+ virial=&(moldyn->atom[i].virial);
+ moldyn->virial+=(virial->xx+virial->yy+virial->zz);
+ moldyn->vir.xx+=virial->xx;
+ moldyn->vir.yy+=virial->yy;
+ moldyn->vir.zz+=virial->zz;
+ moldyn->vir.xy+=virial->xy;
+ moldyn->vir.xz+=virial->xz;
+ moldyn->vir.yz+=virial->yz;
+ }
-double update_e_kin(t_moldyn *moldyn) {
+ /* global virial (absolute coordinates) */
+ virial=&(moldyn->gvir);
+ moldyn->gv=virial->xx+virial->yy+virial->zz;
- return(get_e_kin(moldyn));
+ return moldyn->virial;
}
-double get_total_energy(t_moldyn *moldyn) {
-
- return(moldyn->ekin+moldyn->energy);
-}
+double pressure_calc(t_moldyn *moldyn) {
-t_3dvec get_total_p(t_moldyn *moldyn) {
+ /*
+ * PV = NkT + <W>
+ * with W = 1/3 sum_i f_i r_i (- skipped!)
+ * virial = sum_i f_i r_i
+ *
+ * => P = (2 Ekin + virial) / (3V)
+ */
- t_3dvec p,p_total;
- int i;
- t_atom *atom;
+ /* assume up to date virial & up to date kinetic energy */
- atom=moldyn->atom;
+ /* pressure (atom virials) */
+ moldyn->p=2.0*moldyn->ekin+moldyn->virial;
+ moldyn->p/=(3.0*moldyn->volume);
- v3_zero(&p_total);
- for(i=0;i<moldyn->count;i++) {
- v3_scale(&p,&(atom[i].v),atom[i].mass);
- v3_add(&p_total,&p_total,&p);
- }
+ /* pressure (absolute coordinates) */
+ moldyn->gp=2.0*moldyn->ekin+moldyn->gv;
+ moldyn->gp/=(3.0*moldyn->volume);
- return p_total;
+ return moldyn->p;
}
-double estimate_time_step(t_moldyn *moldyn,double nn_dist) {
+int average_reset(t_moldyn *moldyn) {
- double tau;
+ printf("[moldyn] average reset\n");
- /* nn_dist is the nearest neighbour distance */
+ /* update skip value */
+ moldyn->avg_skip=moldyn->total_steps;
- if(moldyn->t==5.0) {
- printf("[moldyn] i do not estimate timesteps below %f K!\n",
- MOLDYN_CRITICAL_EST_TEMP);
- return 23.42;
- }
+ /* kinetic energy */
+ moldyn->k_sum=0.0;
+ moldyn->k2_sum=0.0;
+
+ /* potential energy */
+ moldyn->v_sum=0.0;
+ moldyn->v2_sum=0.0;
- tau=(0.05*nn_dist*moldyn->atom[0].mass)/sqrt(3.0*K_BOLTZMANN*moldyn->t);
+ /* temperature */
+ moldyn->t_sum=0.0;
- return tau;
+ /* virial */
+ moldyn->virial_sum=0.0;
+ moldyn->gv_sum=0.0;
+
+ /* pressure */
+ moldyn->p_sum=0.0;
+ moldyn->gp_sum=0.0;
+ moldyn->tp_sum=0.0;
+
+ return 0;
}
-/*
- * numerical tricks
- */
+int average_and_fluctuation_calc(t_moldyn *moldyn) {
-/* linked list / cell method */
+ int denom;
-int link_cell_init(t_moldyn *moldyn) {
+ if(moldyn->total_steps<moldyn->avg_skip)
+ return 0;
- t_linkcell *lc;
- int i;
- int fd;
+ denom=moldyn->total_steps+1-moldyn->avg_skip;
+
+ /* assume up to date energies, temperature, pressure etc */
+
+ /* kinetic energy */
+ moldyn->k_sum+=moldyn->ekin;
+ moldyn->k2_sum+=(moldyn->ekin*moldyn->ekin);
+ moldyn->k_avg=moldyn->k_sum/denom;
+ moldyn->k2_avg=moldyn->k2_sum/denom;
+ moldyn->dk2_avg=moldyn->k2_avg-(moldyn->k_avg*moldyn->k_avg);
+
+ /* potential energy */
+ moldyn->v_sum+=moldyn->energy;
+ moldyn->v2_sum+=(moldyn->energy*moldyn->energy);
+ moldyn->v_avg=moldyn->v_sum/denom;
+ moldyn->v2_avg=moldyn->v2_sum/denom;
+ moldyn->dv2_avg=moldyn->v2_avg-(moldyn->v_avg*moldyn->v_avg);
+
+ /* temperature */
+ moldyn->t_sum+=moldyn->t;
+ moldyn->t_avg=moldyn->t_sum/denom;
+
+ /* virial */
+ moldyn->virial_sum+=moldyn->virial;
+ moldyn->virial_avg=moldyn->virial_sum/denom;
+ moldyn->gv_sum+=moldyn->gv;
+ moldyn->gv_avg=moldyn->gv_sum/denom;
+
+ /* pressure */
+ moldyn->p_sum+=moldyn->p;
+ moldyn->p_avg=moldyn->p_sum/denom;
+ moldyn->gp_sum+=moldyn->gp;
+ moldyn->gp_avg=moldyn->gp_sum/denom;
+ moldyn->tp_sum+=moldyn->tp;
+ moldyn->tp_avg=moldyn->tp_sum/denom;
- fd=open("/dev/null",O_WRONLY);
+ return 0;
+}
- lc=&(moldyn->lc);
+int get_heat_capacity(t_moldyn *moldyn) {
- /* partitioning the md cell */
- lc->nx=moldyn->dim.x/moldyn->cutoff;
- lc->x=moldyn->dim.x/lc->nx;
- lc->ny=moldyn->dim.y/moldyn->cutoff;
- lc->y=moldyn->dim.y/lc->ny;
- lc->nz=moldyn->dim.z/moldyn->cutoff;
- lc->z=moldyn->dim.z/lc->nz;
+ double temp2,ighc;
- lc->cells=lc->nx*lc->ny*lc->nz;
- lc->subcell=malloc(lc->cells*sizeof(t_list));
+ /* averages needed for heat capacity calc */
+ if(moldyn->total_steps<moldyn->avg_skip)
+ return 0;
- printf("[moldyn] initializing linked cells (%d)\n",lc->cells);
+ /* (temperature average)^2 */
+ temp2=moldyn->t_avg*moldyn->t_avg;
+ printf("[moldyn] specific heat capacity for T=%f K [J/(kg K)]\n",
+ moldyn->t_avg);
- for(i=0;i<lc->cells;i++)
- //list_init(&(lc->subcell[i]),1);
- list_init(&(lc->subcell[i]),fd);
+ /* ideal gas contribution */
+ ighc=3.0*moldyn->count*K_BOLTZMANN/2.0;
+ printf(" ideal gas contribution: %f\n",
+ ighc/moldyn->mass*KILOGRAM/JOULE);
+
+ /* specific heat for nvt ensemble */
+ moldyn->c_v_nvt=moldyn->dv2_avg/(K_BOLTZMANN*temp2)+ighc;
+ moldyn->c_v_nvt/=moldyn->mass;
+
+ /* specific heat for nve ensemble */
+ moldyn->c_v_nve=ighc/(1.0-(moldyn->dv2_avg/(ighc*K_BOLTZMANN*temp2)));
+ moldyn->c_v_nve/=moldyn->mass;
+
+ printf(" NVE: %f\n",moldyn->c_v_nve*KILOGRAM/JOULE);
+ printf(" NVT: %f\n",moldyn->c_v_nvt*KILOGRAM/JOULE);
+printf(" --> <dV2> sim: %f experimental: %f\n",moldyn->dv2_avg,1.5*moldyn->count*K_B2*moldyn->t_avg*moldyn->t_avg*(1.0-1.5*moldyn->count*K_BOLTZMANN/(700*moldyn->mass*JOULE/KILOGRAM)));
- link_cell_update(moldyn);
-
return 0;
}
-int link_cell_update(t_moldyn *moldyn) {
+double thermodynamic_pressure_calc(t_moldyn *moldyn) {
- int count,i,j,k;
- int nx,ny,nz;
- t_atom *atom;
- t_linkcell *lc;
+ t_3dvec dim;
+ //t_3dvec *tp;
+ double h,dv;
+ double y0,y1;
+ double su,sd;
+ t_atom *store;
- atom=moldyn->atom;
- lc=&(moldyn->lc);
+ /*
+ * dU = - p dV
+ *
+ * => p = - dU/dV
+ *
+ */
- nx=lc->nx;
- ny=lc->ny;
- nz=lc->nz;
+ /* store atomic configuration + dimension */
+ store=malloc(moldyn->count*sizeof(t_atom));
+ if(store==NULL) {
+ printf("[moldyn] allocating store mem failed\n");
+ return -1;
+ }
+ memcpy(store,moldyn->atom,moldyn->count*sizeof(t_atom));
+ dim=moldyn->dim;
+
+ /* x1, y1 */
+ sd=0.00001;
+ h=(1.0-sd)*(1.0-sd)*(1.0-sd);
+ su=pow(2.0-h,ONE_THIRD)-1.0;
+ dv=(1.0-h)*moldyn->volume;
+
+ /* scale up dimension and atom positions */
+ scale_dim(moldyn,SCALE_UP,su,TRUE,TRUE,TRUE);
+ scale_atoms(moldyn,SCALE_UP,su,TRUE,TRUE,TRUE);
+ link_cell_shutdown(moldyn);
+ link_cell_init(moldyn,QUIET);
+ potential_force_calc(moldyn);
+ y1=moldyn->energy;
- for(i=0;i<lc->cells;i++)
- list_destroy(&(moldyn->lc.subcell[i]));
+ /* restore atomic configuration + dim */
+ memcpy(moldyn->atom,store,moldyn->count*sizeof(t_atom));
+ moldyn->dim=dim;
+
+ /* scale down dimension and atom positions */
+ scale_dim(moldyn,SCALE_DOWN,sd,TRUE,TRUE,TRUE);
+ scale_atoms(moldyn,SCALE_DOWN,sd,TRUE,TRUE,TRUE);
+ link_cell_shutdown(moldyn);
+ link_cell_init(moldyn,QUIET);
+ potential_force_calc(moldyn);
+ y0=moldyn->energy;
- for(count=0;count<moldyn->count;count++) {
- i=(atom[count].r.x+(moldyn->dim.x/2))/lc->x;
- j=(atom[count].r.y+(moldyn->dim.y/2))/lc->y;
- k=(atom[count].r.z+(moldyn->dim.z/2))/lc->z;
- list_add_immediate_ptr(&(moldyn->lc.subcell[i+j*nx+k*nx*ny]),
- &(atom[count]));
- }
+ /* calculate pressure */
+ moldyn->tp=-(y1-y0)/(2.0*dv);
- return 0;
+ /* restore atomic configuration */
+ memcpy(moldyn->atom,store,moldyn->count*sizeof(t_atom));
+ moldyn->dim=dim;
+ link_cell_shutdown(moldyn);
+ link_cell_init(moldyn,QUIET);
+ //potential_force_calc(moldyn);
+
+ /* free store buffer */
+ if(store)
+ free(store);
+
+ return moldyn->tp;
}
-int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,t_list *cell) {
+double get_pressure(t_moldyn *moldyn) {
- t_linkcell *lc;
- int a;
- int count1,count2;
- int ci,cj,ck;
- int nx,ny,nz;
- int x,y,z;
- u8 bx,by,bz;
+ return moldyn->p;
- lc=&(moldyn->lc);
- nx=lc->nx;
- ny=lc->ny;
+}
+
+int scale_dim(t_moldyn *moldyn,u8 dir,double scale,u8 x,u8 y,u8 z) {
+
+ t_3dvec *dim;
+
+ dim=&(moldyn->dim);
+
+ if(dir==SCALE_UP)
+ scale=1.0+scale;
+
+ if(dir==SCALE_DOWN)
+ scale=1.0-scale;
+
+ if(x) dim->x*=scale;
+ if(y) dim->y*=scale;
+ if(z) dim->z*=scale;
+
+ return 0;
+}
+
+int scale_atoms(t_moldyn *moldyn,u8 dir,double scale,u8 x,u8 y,u8 z) {
+
+ int i;
+ t_3dvec *r;
+
+ if(dir==SCALE_UP)
+ scale=1.0+scale;
+
+ if(dir==SCALE_DOWN)
+ scale=1.0-scale;
+
+ for(i=0;i<moldyn->count;i++) {
+ r=&(moldyn->atom[i].r);
+ if(x) r->x*=scale;
+ if(y) r->y*=scale;
+ if(z) r->z*=scale;
+ }
+
+ return 0;
+}
+
+int scale_volume(t_moldyn *moldyn) {
+
+ t_3dvec *dim,*vdim;
+ double scale;
+ t_linkcell *lc;
+
+ vdim=&(moldyn->vis.dim);
+ dim=&(moldyn->dim);
+ lc=&(moldyn->lc);
+
+ /* scaling factor */
+ if(moldyn->pt_scale&P_SCALE_BERENDSEN) {
+ scale=1.0-(moldyn->p_ref-moldyn->p)*moldyn->p_tc;
+ scale=pow(scale,ONE_THIRD);
+ }
+ else {
+ scale=pow(moldyn->p/moldyn->p_ref,ONE_THIRD);
+ }
+
+ /* scale the atoms and dimensions */
+ scale_atoms(moldyn,SCALE_DIRECT,scale,TRUE,TRUE,TRUE);
+ scale_dim(moldyn,SCALE_DIRECT,scale,TRUE,TRUE,TRUE);
+
+ /* visualize dimensions */
+ if(vdim->x!=0) {
+ vdim->x=dim->x;
+ vdim->y=dim->y;
+ vdim->z=dim->z;
+ }
+
+ /* recalculate scaled volume */
+ moldyn->volume=dim->x*dim->y*dim->z;
+
+ /* adjust/reinit linkcell */
+ if(((int)(dim->x/moldyn->cutoff)!=lc->nx)||
+ ((int)(dim->y/moldyn->cutoff)!=lc->ny)||
+ ((int)(dim->z/moldyn->cutoff)!=lc->nx)) {
+ link_cell_shutdown(moldyn);
+ link_cell_init(moldyn,QUIET);
+ } else {
+ lc->x*=scale;
+ lc->y*=scale;
+ lc->z*=scale;
+ }
+
+ return 0;
+
+}
+
+double e_kin_calc(t_moldyn *moldyn) {
+
+ int i;
+ t_atom *atom;
+
+ atom=moldyn->atom;
+ moldyn->ekin=0.0;
+
+ for(i=0;i<moldyn->count;i++) {
+ atom[i].ekin=0.5*atom[i].mass*v3_absolute_square(&(atom[i].v));
+ moldyn->ekin+=atom[i].ekin;
+ }
+
+ return moldyn->ekin;
+}
+
+double get_total_energy(t_moldyn *moldyn) {
+
+ return(moldyn->ekin+moldyn->energy);
+}
+
+t_3dvec get_total_p(t_moldyn *moldyn) {
+
+ t_3dvec p,p_total;
+ int i;
+ t_atom *atom;
+
+ atom=moldyn->atom;
+
+ v3_zero(&p_total);
+ for(i=0;i<moldyn->count;i++) {
+ v3_scale(&p,&(atom[i].v),atom[i].mass);
+ v3_add(&p_total,&p_total,&p);
+ }
+
+ return p_total;
+}
+
+double estimate_time_step(t_moldyn *moldyn,double nn_dist) {
+
+ double tau;
+
+ /* nn_dist is the nearest neighbour distance */
+
+ tau=(0.05*nn_dist*moldyn->atom[0].mass)/sqrt(3.0*K_BOLTZMANN*moldyn->t);
+
+ return tau;
+}
+
+/*
+ * numerical tricks
+ */
+
+/* linked list / cell method */
+
+int link_cell_init(t_moldyn *moldyn,u8 vol) {
+
+ t_linkcell *lc;
+ int i;
+
+ lc=&(moldyn->lc);
+
+ /* partitioning the md cell */
+ lc->nx=moldyn->dim.x/moldyn->cutoff;
+ lc->x=moldyn->dim.x/lc->nx;
+ lc->ny=moldyn->dim.y/moldyn->cutoff;
+ lc->y=moldyn->dim.y/lc->ny;
+ lc->nz=moldyn->dim.z/moldyn->cutoff;
+ lc->z=moldyn->dim.z/lc->nz;
+ lc->cells=lc->nx*lc->ny*lc->nz;
+
+#ifdef STATIC_LISTS
+ lc->subcell=malloc(lc->cells*sizeof(int*));
+#else
+ lc->subcell=malloc(lc->cells*sizeof(t_list));
+#endif
+
+ if(lc->subcell==NULL) {
+ perror("[moldyn] cell init (malloc)");
+ return -1;
+ }
+
+ if(lc->cells<27)
+ printf("[moldyn] FATAL: less then 27 subcells!\n");
+
+ if(vol) {
+#ifdef STATIC_LISTS
+ printf("[moldyn] initializing 'static' linked cells (%d)\n",
+ lc->cells);
+#else
+ printf("[moldyn] initializing 'dynamic' linked cells (%d)\n",
+ lc->cells);
+#endif
+ printf(" x: %d x %f A\n",lc->nx,lc->x);
+ printf(" y: %d x %f A\n",lc->ny,lc->y);
+ printf(" z: %d x %f A\n",lc->nz,lc->z);
+ }
+
+#ifdef STATIC_LISTS
+ /* list init */
+ for(i=0;i<lc->cells;i++) {
+ lc->subcell[i]=malloc((MAX_ATOMS_PER_LIST+1)*sizeof(int));
+ if(lc->subcell[i]==NULL) {
+ perror("[moldyn] list init (malloc)");
+ return -1;
+ }
+ /*
+ if(i==0)
+ printf(" ---> %d malloc %p (%p)\n",
+ i,lc->subcell[0],lc->subcell);
+ */
+ }
+#else
+ for(i=0;i<lc->cells;i++)
+ list_init_f(&(lc->subcell[i]));
+#endif
+
+ /* update the list */
+ link_cell_update(moldyn);
+
+ return 0;
+}
+
+int link_cell_update(t_moldyn *moldyn) {
+
+ int count,i,j,k;
+ int nx,ny;
+ t_atom *atom;
+ t_linkcell *lc;
+#ifdef STATIC_LISTS
+ int p;
+#endif
+
+ atom=moldyn->atom;
+ lc=&(moldyn->lc);
+
+ nx=lc->nx;
+ ny=lc->ny;
+
+ for(i=0;i<lc->cells;i++)
+#ifdef STATIC_LISTS
+ memset(lc->subcell[i],0,(MAX_ATOMS_PER_LIST+1)*sizeof(int));
+#else
+ list_destroy_f(&(lc->subcell[i]));
+#endif
+
+ for(count=0;count<moldyn->count;count++) {
+ i=((atom[count].r.x+(moldyn->dim.x/2))/lc->x);
+ j=((atom[count].r.y+(moldyn->dim.y/2))/lc->y);
+ k=((atom[count].r.z+(moldyn->dim.z/2))/lc->z);
+
+#ifdef STATIC_LISTS
+ p=0;
+ while(lc->subcell[i+j*nx+k*nx*ny][p]!=0)
+ p++;
+
+ if(p>=MAX_ATOMS_PER_LIST) {
+ printf("[moldyn] FATAL: amount of atoms too high!\n");
+ return -1;
+ }
+
+ lc->subcell[i+j*nx+k*nx*ny][p]=count;
+#else
+ list_add_immediate_f(&(lc->subcell[i+j*nx+k*nx*ny]),
+ &(atom[count]));
+ /*
+ if(j==0&&k==0)
+ printf(" ---> %d %d malloc %p (%p)\n",
+ i,count,lc->subcell[i].current,lc->subcell);
+ */
+#endif
+ }
+
+ return 0;
+}
+
+int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,
+#ifdef STATIC_LISTS
+ int **cell
+#else
+ t_list *cell
+#endif
+ ) {
+
+ t_linkcell *lc;
+ int a;
+ int count1,count2;
+ int ci,cj,ck;
+ int nx,ny,nz;
+ int x,y,z;
+ u8 bx,by,bz;
+
+ lc=&(moldyn->lc);
+ nx=lc->nx;
+ ny=lc->ny;
nz=lc->nz;
count1=1;
count2=27;
a=nx*ny;
+ if(i>=nx||j>=ny||k>=nz)
+ printf("[moldyn] WARNING: lcni %d/%d %d/%d %d/%d\n",
+ i,nx,j,ny,k,nz);
+
cell[0]=lc->subcell[i+j*nx+k*a];
for(ci=-1;ci<=1;ci++) {
bx=0;
}
lc->dnlc=count1;
- lc->countn=27;
- return count2;
+ return count1;
}
int link_cell_shutdown(t_moldyn *moldyn) {
lc=&(moldyn->lc);
- for(i=0;i<lc->nx*lc->ny*lc->nz;i++)
- list_shutdown(&(moldyn->lc.subcell[i]));
+ for(i=0;i<lc->cells;i++) {
+#ifdef STATIC_LISTS
+ free(lc->subcell[i]);
+#else
+ //printf(" ---> %d free %p\n",i,lc->subcell[i].start);
+ list_destroy_f(&(lc->subcell[i]));
+#endif
+ }
+
+ free(lc->subcell);
return 0;
}
t_moldyn_schedule *schedule;
schedule=&(moldyn->schedule);
- count=++(schedule->content_count);
+ count=++(schedule->total_sched);
- ptr=realloc(moldyn->schedule.runs,count*sizeof(int));
+ ptr=realloc(schedule->runs,count*sizeof(int));
if(!ptr) {
perror("[moldyn] realloc (runs)");
return -1;
}
- moldyn->schedule.runs=ptr;
- moldyn->schedule.runs[count-1]=runs;
+ schedule->runs=ptr;
+ schedule->runs[count-1]=runs;
ptr=realloc(schedule->tau,count*sizeof(double));
if(!ptr) {
perror("[moldyn] realloc (tau)");
return -1;
}
- moldyn->schedule.tau=ptr;
- moldyn->schedule.tau[count-1]=tau;
+ schedule->tau=ptr;
+ schedule->tau[count-1]=tau;
+
+ printf("[moldyn] schedule added:\n");
+ printf(" number: %d | runs: %d | tau: %f\n",count-1,runs,tau);
+
return 0;
}
-int moldyn_set_schedule_hook(t_moldyn *moldyn,void *hook,void *hook_params) {
+int moldyn_set_schedule_hook(t_moldyn *moldyn,set_hook hook,void *hook_params) {
moldyn->schedule.hook=hook;
moldyn->schedule.hook_params=hook_params;
int moldyn_integrate(t_moldyn *moldyn) {
- int i,sched;
- unsigned int e,m,s,v;
- t_3dvec p;
- t_moldyn_schedule *schedule;
+ int i;
+ unsigned int e,m,s,v,p,t,a;
+ t_3dvec momentum;
+ t_moldyn_schedule *sched;
t_atom *atom;
int fd;
- char fb[128];
+ char dir[128];
double ds;
+ double energy_scale;
+ struct timeval t1,t2;
+ //double tp;
- schedule=&(moldyn->schedule);
+ sched=&(moldyn->schedule);
atom=moldyn->atom;
/* initialize linked cell method */
- link_cell_init(moldyn);
+ link_cell_init(moldyn,VERBOSE);
/* logging & visualization */
e=moldyn->ewrite;
m=moldyn->mwrite;
s=moldyn->swrite;
v=moldyn->vwrite;
+ a=moldyn->awrite;
+ p=moldyn->pwrite;
+ t=moldyn->twrite;
/* sqaure of some variables */
moldyn->tau_square=moldyn->tau*moldyn->tau;
moldyn->cutoff_square=moldyn->cutoff*moldyn->cutoff;
+
+ /* get current time */
+ gettimeofday(&t1,NULL);
+
/* calculate initial forces */
potential_force_calc(moldyn);
+#ifdef DEBUG
+//return 0;
+#endif
- /* do some checks before we actually start calculating bullshit */
+ /* some stupid checks before we actually start calculating bullshit */
if(moldyn->cutoff>0.5*moldyn->dim.x)
- printf("[moldyn] warning: cutoff > 0.5 x dim.x\n");
+ printf("[moldyn] WARNING: cutoff > 0.5 x dim.x\n");
if(moldyn->cutoff>0.5*moldyn->dim.y)
- printf("[moldyn] warning: cutoff > 0.5 x dim.y\n");
+ printf("[moldyn] WARNING: cutoff > 0.5 x dim.y\n");
if(moldyn->cutoff>0.5*moldyn->dim.z)
- printf("[moldyn] warning: cutoff > 0.5 x dim.z\n");
+ printf("[moldyn] WARNING: cutoff > 0.5 x dim.z\n");
ds=0.5*atom[0].f.x*moldyn->tau_square/atom[0].mass;
if(ds>0.05*moldyn->nnd)
- printf("[moldyn] warning: forces too high / tau too small!\n");
+ printf("[moldyn] WARNING: forces too high / tau too small!\n");
/* zero absolute time */
moldyn->time=0.0;
- for(sched=0;sched<moldyn->schedule.content_count;sched++) {
+ moldyn->total_steps=0;
+
+ /* debugging, ignore */
+ moldyn->debug=0;
+
+ /* tell the world */
+ printf("[moldyn] integration start, go get a coffee ...\n");
+
+ /* executing the schedule */
+ sched->count=0;
+ while(sched->count<sched->total_sched) {
/* setting amount of runs and finite time step size */
- moldyn->tau=schedule->tau[sched];
+ moldyn->tau=sched->tau[sched->count];
moldyn->tau_square=moldyn->tau*moldyn->tau;
- moldyn->time_steps=schedule->runs[sched];
+ moldyn->time_steps=sched->runs[sched->count];
+
+ /* energy scaling factor (might change!) */
+ energy_scale=moldyn->count*EV;
/* integration according to schedule */
/* integration step */
moldyn->integrate(moldyn);
+ /* calculate kinetic energy, temperature and pressure */
+ e_kin_calc(moldyn);
+ temperature_calc(moldyn);
+ virial_sum(moldyn);
+ pressure_calc(moldyn);
+ //thermodynamic_pressure_calc(moldyn);
+
+ /* calculate fluctuations + averages */
+ average_and_fluctuation_calc(moldyn);
+
/* p/t scaling */
if(moldyn->pt_scale&(T_SCALE_BERENDSEN|T_SCALE_DIRECT))
scale_velocity(moldyn,FALSE);
-
- /* increase absolute time */
- moldyn->time+=moldyn->tau;
+ if(moldyn->pt_scale&(P_SCALE_BERENDSEN|P_SCALE_DIRECT))
+ scale_volume(moldyn);
/* check for log & visualization */
if(e) {
- if(!(i%e))
+ if(!(moldyn->total_steps%e))
dprintf(moldyn->efd,
- "%.15f %.45f %.45f %.45f\n",
- moldyn->time,update_e_kin(moldyn),
- moldyn->energy,
- get_total_energy(moldyn));
+ "%f %f %f %f\n",
+ moldyn->time,moldyn->ekin/energy_scale,
+ moldyn->energy/energy_scale,
+ get_total_energy(moldyn)/energy_scale);
}
if(m) {
- if(!(i%m)) {
- p=get_total_p(moldyn);
+ if(!(moldyn->total_steps%m)) {
+ momentum=get_total_p(moldyn);
dprintf(moldyn->mfd,
- "%.15f %.45f\n",moldyn->time,
- v3_norm(&p));
+ "%f %f %f %f %f\n",moldyn->time,
+ momentum.x,momentum.y,momentum.z,
+ v3_norm(&momentum));
+ }
+ }
+ if(p) {
+ if(!(moldyn->total_steps%p)) {
+ dprintf(moldyn->pfd,
+ "%f %f %f %f %f %f %f\n",moldyn->time,
+ moldyn->p/BAR,moldyn->p_avg/BAR,
+ moldyn->gp/BAR,moldyn->gp_avg/BAR,
+ moldyn->tp/BAR,moldyn->tp_avg/BAR);
+ }
+ }
+ if(t) {
+ if(!(moldyn->total_steps%t)) {
+ dprintf(moldyn->tfd,
+ "%f %f %f\n",
+ moldyn->time,moldyn->t,moldyn->t_avg);
+ }
+ }
+ if(v) {
+ if(!(moldyn->total_steps%v)) {
+ dprintf(moldyn->vfd,
+ "%f %f\n",moldyn->time,moldyn->volume);
}
}
if(s) {
- if(!(i%s)) {
- snprintf(fb,128,"%s-%f-%.15f.save",moldyn->sfb,
- moldyn->t,i*moldyn->tau);
- fd=open(fb,O_WRONLY|O_TRUNC|O_CREAT);
+ if(!(moldyn->total_steps%s)) {
+ snprintf(dir,128,"%s/s-%07.f.save",
+ moldyn->vlsdir,moldyn->time);
+ fd=open(dir,O_WRONLY|O_TRUNC|O_CREAT,
+ S_IRUSR|S_IWUSR);
if(fd<0) perror("[moldyn] save fd open");
else {
write(fd,moldyn,sizeof(t_moldyn));
close(fd);
}
}
- if(v) {
- if(!(i%v)) {
- visual_atoms(&(moldyn->vis),moldyn->time,
- moldyn->atom,moldyn->count);
- printf("\rsched: %d, steps: %d",sched,i);
- fflush(stdout);
+ if(a) {
+ if(!(moldyn->total_steps%a)) {
+ visual_atoms(moldyn);
}
}
+ /* display progress */
+ //if(!(moldyn->total_steps%10)) {
+ /* get current time */
+ gettimeofday(&t2,NULL);
+
+printf("\rsched:%d, steps:%d/%d, T:%4.1f/%4.1f P:%4.1f/%4.1f V:%6.1f (%d)",
+ sched->count,i,moldyn->total_steps,
+ moldyn->t,moldyn->t_avg,
+ moldyn->p/BAR,moldyn->p_avg/BAR,
+ moldyn->volume,
+ (int)(t2.tv_sec-t1.tv_sec));
+
+ fflush(stdout);
+
+ /* copy over time */
+ t1=t2;
+ //}
+
+ /* increase absolute time */
+ moldyn->time+=moldyn->tau;
+ moldyn->total_steps+=1;
+
}
/* check for hooks */
- if(schedule->hook)
- schedule->hook(moldyn,schedule->hook_params);
+ if(sched->hook) {
+ printf("\n ## schedule hook %d start ##\n",
+ sched->count);
+ sched->hook(moldyn,sched->hook_params);
+ printf(" ## schedule hook end ##\n");
+ }
+
+ /* increase the schedule counter */
+ sched->count+=1;
}
int velocity_verlet(t_moldyn *moldyn) {
int i,count;
- double tau,tau_square;
+ double tau,tau_square,h;
t_3dvec delta;
t_atom *atom;
tau_square=moldyn->tau_square;
for(i=0;i<count;i++) {
+ /* check whether fixed atom */
+ if(atom[i].attr&ATOM_ATTR_FP)
+ continue;
/* new positions */
+ h=0.5/atom[i].mass;
v3_scale(&delta,&(atom[i].v),tau);
v3_add(&(atom[i].r),&(atom[i].r),&delta);
- v3_scale(&delta,&(atom[i].f),0.5*tau_square/atom[i].mass);
+ v3_scale(&delta,&(atom[i].f),h*tau_square);
v3_add(&(atom[i].r),&(atom[i].r),&delta);
check_per_bound(moldyn,&(atom[i].r));
- /* velocities */
- v3_scale(&delta,&(atom[i].f),0.5*tau/atom[i].mass);
+ /* velocities [actually v(t+tau/2)] */
+ v3_scale(&delta,&(atom[i].f),h*tau);
v3_add(&(atom[i].v),&(atom[i].v),&delta);
}
+ /* criticial check */
+ moldyn_bc_check(moldyn);
+
/* neighbour list update */
link_cell_update(moldyn);
/* forces depending on chosen potential */
potential_force_calc(moldyn);
- //moldyn->potential_force_function(moldyn);
for(i=0;i<count;i++) {
- /* again velocities */
+ /* check whether fixed atom */
+ if(atom[i].attr&ATOM_ATTR_FP)
+ continue;
+ /* again velocities [actually v(t+tau)] */
v3_scale(&delta,&(atom[i].f),0.5*tau/atom[i].mass);
v3_add(&(atom[i].v),&(atom[i].v),&delta);
}
/*
*
- * potentials & corresponding forces
+ * potentials & corresponding forces & virial routine
*
*/
int i,j,k,count;
t_atom *itom,*jtom,*ktom;
+ t_virial *virial;
t_linkcell *lc;
+#ifdef STATIC_LISTS
+ int *neighbour_i[27];
+ int p,q;
+ t_atom *atom;
+#else
t_list neighbour_i[27];
t_list neighbour_i2[27];
- //t_list neighbour_j[27];
t_list *this,*that;
- u8 bc_ij,bc_ijk;
- int countn,dnlc;
+#endif
+ u8 bc_ij,bc_ik;
+ int dnlc;
count=moldyn->count;
itom=moldyn->atom;
lc=&(moldyn->lc);
+#ifdef STATIC_LISTS
+ atom=moldyn->atom;
+#endif
/* reset energy */
moldyn->energy=0.0;
+ /* reset global virial */
+ memset(&(moldyn->gvir),0,sizeof(t_virial));
+
+ /* reset force, site energy and virial of every atom */
for(i=0;i<count;i++) {
/* reset force */
v3_zero(&(itom[i].f));
+ /* reset virial */
+ virial=(&(itom[i].virial));
+ virial->xx=0.0;
+ virial->yy=0.0;
+ virial->zz=0.0;
+ virial->xy=0.0;
+ virial->xz=0.0;
+ virial->yz=0.0;
+
+ /* reset site energy */
+ itom[i].e=0.0;
+
+ }
+
+ /* get energy, force and virial of every atom */
+
+ /* first (and only) loop over atoms i */
+ for(i=0;i<count;i++) {
+
/* single particle potential/force */
if(itom[i].attr&ATOM_ATTR_1BP)
- moldyn->func1b(moldyn,&(itom[i]));
+ if(moldyn->func1b)
+ moldyn->func1b(moldyn,&(itom[i]));
+
+ if(!(itom[i].attr&(ATOM_ATTR_2BP|ATOM_ATTR_3BP)))
+ continue;
/* 2 body pair potential/force */
- if(itom[i].attr&(ATOM_ATTR_2BP|ATOM_ATTR_3BP)) {
- link_cell_neighbour_index(moldyn,
- (itom[i].r.x+moldyn->dim.x/2)/lc->x,
- (itom[i].r.y+moldyn->dim.y/2)/lc->y,
- (itom[i].r.z+moldyn->dim.z/2)/lc->z,
- neighbour_i);
+ link_cell_neighbour_index(moldyn,
+ (itom[i].r.x+moldyn->dim.x/2)/lc->x,
+ (itom[i].r.y+moldyn->dim.y/2)/lc->y,
+ (itom[i].r.z+moldyn->dim.z/2)/lc->z,
+ neighbour_i);
+
+ dnlc=lc->dnlc;
+
+ /* first loop over atoms j */
+ if(moldyn->func2b) {
+ for(j=0;j<27;j++) {
+
+ bc_ij=(j<dnlc)?0:1;
+#ifdef STATIC_LISTS
+ p=0;
- countn=lc->countn;
- dnlc=lc->dnlc;
+ while(neighbour_i[j][p]!=0) {
- for(j=0;j<countn;j++) {
+ jtom=&(atom[neighbour_i[j][p]]);
+ p++;
+ if(jtom==&(itom[i]))
+ continue;
+
+ if((jtom->attr&ATOM_ATTR_2BP)&
+ (itom[i].attr&ATOM_ATTR_2BP)) {
+ moldyn->func2b(moldyn,
+ &(itom[i]),
+ jtom,
+ bc_ij);
+ }
+ }
+#else
this=&(neighbour_i[j]);
- list_reset(this);
+ list_reset_f(this);
if(this->start==NULL)
continue;
- bc_ij=(j<dnlc)?0:1;
-
do {
jtom=this->current->data;
continue;
if((jtom->attr&ATOM_ATTR_2BP)&
- (itom[i].attr&ATOM_ATTR_2BP))
+ (itom[i].attr&ATOM_ATTR_2BP)) {
moldyn->func2b(moldyn,
&(itom[i]),
jtom,
- bc_ij);
+ bc_ij);
+ }
+ } while(list_next_f(this)!=L_NO_NEXT_ELEMENT);
+#endif
- /* 3 body potential/force */
+ }
+ }
- if(!(itom[i].attr&ATOM_ATTR_3BP)||
- !(jtom->attr&ATOM_ATTR_3BP))
- continue;
+ /* 3 body potential/force */
+
+ if(!(itom[i].attr&ATOM_ATTR_3BP))
+ continue;
+
+ /* copy the neighbour lists */
+#ifdef STATIC_LISTS
+ /* no copy needed for static lists */
+#else
+ memcpy(neighbour_i2,neighbour_i,27*sizeof(t_list));
+#endif
+
+ /* second loop over atoms j */
+ for(j=0;j<27;j++) {
+
+ bc_ij=(j<dnlc)?0:1;
+#ifdef STATIC_LISTS
+ p=0;
+
+ while(neighbour_i[j][p]!=0) {
+
+ jtom=&(atom[neighbour_i[j][p]]);
+ p++;
+#else
+ this=&(neighbour_i[j]);
+ list_reset_f(this);
+
+ if(this->start==NULL)
+ continue;
+
+ do {
+
+ jtom=this->current->data;
+#endif
+
+ if(jtom==&(itom[i]))
+ continue;
+
+ if(!(jtom->attr&ATOM_ATTR_3BP))
+ continue;
+
+ /* reset 3bp run */
+ moldyn->run3bp=1;
+
+ if(moldyn->func3b_j1)
+ moldyn->func3b_j1(moldyn,
+ &(itom[i]),
+ jtom,
+ bc_ij);
- /* neighbourhood of atom j is not needed! */
-
- // link_cell_neighbour_index(moldyn,
- // (jtom->r.x+moldyn->dim.x/2)/lc->x,
- // (jtom->r.y+moldyn->dim.y/2)/lc->y,
- // (jtom->r.z+moldyn->dim.z/2)/lc->z,
- // neighbour_j);
-
-// /* neighbours of j */
-// for(k=0;k<lc->countn;k++) {
-//
-// that=&(neighbour_j[k]);
-// list_reset(that);
-//
-// if(that->start==NULL)
-// continue;
-//
-// bc_ijk=(k<lc->dnlc)?0:1;
-//
-// do {
-//
-// ktom=that->current->data;
-//
-// if(!(ktom->attr&ATOM_ATTR_3BP))
-// continue;
-//
-// if(ktom==jtom)
-// continue;
-//
-// if(ktom==&(itom[i]))
-// continue;
-//
-// moldyn->func3b(moldyn,&(itom[i]),jtom,ktom,bc_ijk);
-//
-/* } while(list_next(that)!=\ */
-// L_NO_NEXT_ELEMENT);
-//
-// }
+ /* in first j loop, 3bp run can be skipped */
+ if(!(moldyn->run3bp))
+ continue;
- /* copy the neighbour lists */
- memcpy(neighbour_i2,neighbour_i,
- 27*sizeof(t_list));
+ /* first loop over atoms k */
+ if(moldyn->func3b_k1) {
+
+ for(k=0;k<27;k++) {
- /* get neighbours of i */
- for(k=0;k<countn;k++) {
+ bc_ik=(k<dnlc)?0:1;
+#ifdef STATIC_LISTS
+ q=0;
- that=&(neighbour_i2[k]);
- list_reset(that);
+ while(neighbour_i[j][q]!=0) {
+
+ ktom=&(atom[neighbour_i[k][q]]);
+ q++;
+#else
+ that=&(neighbour_i2[k]);
+ list_reset_f(that);
- if(that->start==NULL)
+ if(that->start==NULL)
+ continue;
+
+ do {
+ ktom=that->current->data;
+#endif
+
+ if(!(ktom->attr&ATOM_ATTR_3BP))
+ continue;
+
+ if(ktom==jtom)
continue;
- bc_ijk=(k<dnlc)?0:1;
+ if(ktom==&(itom[i]))
+ continue;
- do {
+ moldyn->func3b_k1(moldyn,
+ &(itom[i]),
+ jtom,
+ ktom,
+ bc_ik|bc_ij);
+#ifdef STATIC_LISTS
+ }
+#else
+ } while(list_next_f(that)!=\
+ L_NO_NEXT_ELEMENT);
+#endif
- ktom=that->current->data;
+ }
- if(!(ktom->attr&ATOM_ATTR_3BP))
- continue;
+ }
- if(ktom==jtom)
- continue;
+ if(moldyn->func3b_j2)
+ moldyn->func3b_j2(moldyn,
+ &(itom[i]),
+ jtom,
+ bc_ij);
- if(ktom==&(itom[i]))
- continue;
+ /* second loop over atoms k */
+ if(moldyn->func3b_k2) {
-//printf("Debug: atom %d before 3bp: %08x %08x %08x | %.15f %.15f %.15f\n",i,&itom[i],jtom,ktom,itom[i].r.x,itom[i].f.x,itom[i].v.x);
- moldyn->func3b(moldyn,&(itom[i]),jtom,ktom,bc_ijk);
-//printf("Debug: atom %d after 3bp: %08x %08x %08x | %.15f %.15f %.15f\n",i,&itom[i],jtom,ktom,itom[i].r.x,itom[i].f.x,itom[i].v.x);
+ for(k=0;k<27;k++) {
- } while(list_next(that)!=\
- L_NO_NEXT_ELEMENT);
+ bc_ik=(k<dnlc)?0:1;
+#ifdef STATIC_LISTS
+ q=0;
- }
+ while(neighbour_i[j][q]!=0) {
+
+ ktom=&(atom[neighbour_i[k][q]]);
+ q++;
+#else
+ that=&(neighbour_i2[k]);
+ list_reset_f(that);
- } while(list_next(this)!=L_NO_NEXT_ELEMENT);
-
- /* 2bp post function */
- if(moldyn->func2b_post)
- moldyn->func2b_post(moldyn,
- &(itom[i]),
- jtom,bc_ij);
+ if(that->start==NULL)
+ continue;
+
+ do {
+ ktom=that->current->data;
+#endif
+
+ if(!(ktom->attr&ATOM_ATTR_3BP))
+ continue;
+
+ if(ktom==jtom)
+ continue;
+
+ if(ktom==&(itom[i]))
+ continue;
+
+ moldyn->func3b_k2(moldyn,
+ &(itom[i]),
+ jtom,
+ ktom,
+ bc_ik|bc_ij);
+
+#ifdef STATIC_LISTS
+ }
+#else
+ } while(list_next_f(that)!=\
+ L_NO_NEXT_ELEMENT);
+#endif
+
+ }
+
+ }
+ /* 2bp post function */
+ if(moldyn->func3b_j3) {
+ moldyn->func3b_j3(moldyn,
+ &(itom[i]),
+ jtom,bc_ij);
+ }
+#ifdef STATIC_LISTS
}
+#else
+ } while(list_next_f(this)!=L_NO_NEXT_ELEMENT);
+#endif
+
}
+
+#ifdef DEBUG
+ //printf("\n\n");
+#endif
+#ifdef VDEBUG
+ printf("\n\n");
+#endif
+
+ }
+
+#ifdef DEBUG
+ //printf("\nATOM 0: %f %f %f\n\n",itom->f.x,itom->f.y,itom->f.z);
+ if(moldyn->time>DSTART&&moldyn->time<DEND) {
+ printf("force:\n");
+ printf(" x: %0.40f\n",moldyn->atom[DATOM].f.x);
+ printf(" y: %0.40f\n",moldyn->atom[DATOM].f.y);
+ printf(" z: %0.40f\n",moldyn->atom[DATOM].f.z);
+ }
+#endif
+
+ /* some postprocessing */
+ for(i=0;i<count;i++) {
+ /* calculate global virial */
+ moldyn->gvir.xx+=itom[i].r.x*itom[i].f.x;
+ moldyn->gvir.yy+=itom[i].r.y*itom[i].f.y;
+ moldyn->gvir.zz+=itom[i].r.z*itom[i].f.z;
+ moldyn->gvir.xy+=itom[i].r.y*itom[i].f.x;
+ moldyn->gvir.xz+=itom[i].r.z*itom[i].f.x;
+ moldyn->gvir.yz+=itom[i].r.z*itom[i].f.y;
+
+ /* check forces regarding the given timestep */
+ if(v3_norm(&(itom[i].f))>\
+ 0.1*moldyn->nnd*itom[i].mass/moldyn->tau_square)
+ printf("[moldyn] WARNING: pfc (high force: atom %d)\n",
+ i);
}
return 0;
}
/*
- * periodic boundayr checking
+ * virial calculation
*/
+//inline int virial_calc(t_atom *a,t_3dvec *f,t_3dvec *d) {
+int virial_calc(t_atom *a,t_3dvec *f,t_3dvec *d) {
+
+ a->virial.xx+=f->x*d->x;
+ a->virial.yy+=f->y*d->y;
+ a->virial.zz+=f->z*d->z;
+ a->virial.xy+=f->x*d->y;
+ a->virial.xz+=f->x*d->z;
+ a->virial.yz+=f->y*d->z;
+
+ return 0;
+}
+
+/*
+ * periodic boundary checking
+ */
+
+//inline int check_per_bound(t_moldyn *moldyn,t_3dvec *a) {
int check_per_bound(t_moldyn *moldyn,t_3dvec *a) {
double x,y,z;
dim=&(moldyn->dim);
- x=0.5*dim->x;
- y=0.5*dim->y;
- z=0.5*dim->z;
+ x=dim->x/2;
+ y=dim->y/2;
+ z=dim->z/2;
if(moldyn->status&MOLDYN_STAT_PBX) {
if(a->x>=x) a->x-=dim->x;
return 0;
}
+/*
+ * debugging / critical check functions
+ */
+
+int moldyn_bc_check(t_moldyn *moldyn) {
+
+ t_atom *atom;
+ t_3dvec *dim;
+ int i;
+ double x;
+ u8 byte;
+ int j,k;
+
+ atom=moldyn->atom;
+ dim=&(moldyn->dim);
+ x=dim->x/2;
+
+ for(i=0;i<moldyn->count;i++) {
+ if(atom[i].r.x>=dim->x/2||-atom[i].r.x>dim->x/2) {
+ printf("FATAL: atom %d: x: %.20f (%.20f)\n",
+ i,atom[i].r.x,dim->x/2);
+ printf("diagnostic:\n");
+ printf("-----------\natom.r.x:\n");
+ for(j=0;j<8;j++) {
+ memcpy(&byte,(u8 *)(&(atom[i].r.x))+j,1);
+ for(k=0;k<8;k++)
+ printf("%d%c",
+ ((byte)&(1<<k))?1:0,
+ (k==7)?'\n':'|');
+ }
+ printf("---------------\nx=dim.x/2:\n");
+ for(j=0;j<8;j++) {
+ memcpy(&byte,(u8 *)(&x)+j,1);
+ for(k=0;k<8;k++)
+ printf("%d%c",
+ ((byte)&(1<<k))?1:0,
+ (k==7)?'\n':'|');
+ }
+ if(atom[i].r.x==x) printf("the same!\n");
+ else printf("different!\n");
+ }
+ if(atom[i].r.y>=dim->y/2||-atom[i].r.y>dim->y/2)
+ printf("FATAL: atom %d: y: %.20f (%.20f)\n",
+ i,atom[i].r.y,dim->y/2);
+ if(atom[i].r.z>=dim->z/2||-atom[i].r.z>dim->z/2)
+ printf("FATAL: atom %d: z: %.20f (%.20f)\n",
+ i,atom[i].r.z,dim->z/2);
+ }
+
+ return 0;
+}
/*
- * example potentials
+ * restore function
*/
-/* harmonic oscillator potential and force */
+int moldyn_read_save_file(t_moldyn *moldyn,char *file) {
-int harmonic_oscillator(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
+ int fd;
+ int cnt,size;
+ int fsize;
+ int corr;
+
+ fd=open(file,O_RDONLY);
+ if(fd<0) {
+ perror("[moldyn] load save file open");
+ return fd;
+ }
- t_ho_params *params;
- t_3dvec force,distance;
- double d;
- double sc,equi_dist;
+ fsize=lseek(fd,0,SEEK_END);
+ lseek(fd,0,SEEK_SET);
- params=moldyn->pot2b_params;
- sc=params->spring_constant;
- equi_dist=params->equilibrium_distance;
+ size=sizeof(t_moldyn);
- v3_sub(&distance,&(ai->r),&(aj->r));
-
- if(bc) check_per_bound(moldyn,&distance);
- d=v3_norm(&distance);
- if(d<=moldyn->cutoff) {
- /* energy is 1/2 (d-d0)^2, but we will add this twice ... */
- moldyn->energy+=(0.25*sc*(d-equi_dist)*(d-equi_dist));
- v3_scale(&force,&distance,-sc*(1.0-(equi_dist/d)));
- v3_add(&(ai->f),&(ai->f),&force);
+ while(size) {
+ cnt=read(fd,moldyn,size);
+ if(cnt<0) {
+ perror("[moldyn] load save file read (moldyn)");
+ return cnt;
+ }
+ size-=cnt;
+ }
+
+ size=moldyn->count*sizeof(t_atom);
+
+ /* correcting possible atom data offset */
+ corr=0;
+ if(fsize!=sizeof(t_moldyn)+size) {
+ corr=fsize-sizeof(t_moldyn)-size;
+ printf("[moldyn] WARNING: lsf (illegal file size)\n");
+ printf(" moifying offset:\n");
+ printf(" - current pos: %d\n",sizeof(t_moldyn));
+ printf(" - atom size: %d\n",size);
+ printf(" - file size: %d\n",fsize);
+ printf(" => correction: %d\n",corr);
+ lseek(fd,corr,SEEK_CUR);
}
+ moldyn->atom=(t_atom *)malloc(size);
+ if(moldyn->atom==NULL) {
+ perror("[moldyn] load save file malloc (atoms)");
+ return -1;
+ }
+
+ while(size) {
+ cnt=read(fd,moldyn->atom,size);
+ if(cnt<0) {
+ perror("[moldyn] load save file read (atoms)");
+ return cnt;
+ }
+ size-=cnt;
+ }
+
+ // hooks etc ...
+
return 0;
}
-/* lennard jones potential & force for one sort of atoms */
-
-int lennard_jones(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
-
- t_lj_params *params;
- t_3dvec force,distance;
- double d,h1,h2;
- double eps,sig6,sig12;
-
- params=moldyn->pot2b_params;
- eps=params->epsilon4;
- sig6=params->sigma6;
- sig12=params->sigma12;
-
- v3_sub(&distance,&(ai->r),&(aj->r));
- if(bc) check_per_bound(moldyn,&distance);
- d=v3_absolute_square(&distance); /* 1/r^2 */
- if(d<=moldyn->cutoff_square) {
- d=1.0/d; /* 1/r^2 */
- h2=d*d; /* 1/r^4 */
- h2*=d; /* 1/r^6 */
- h1=h2*h2; /* 1/r^12 */
- /* energy is eps*..., but we will add this twice ... */
- moldyn->energy+=0.5*eps*(sig12*h1-sig6*h2);
- h2*=d; /* 1/r^8 */
- h1*=d; /* 1/r^14 */
- h2*=6*sig6;
- h1*=12*sig12;
- d=+h1-h2;
- d*=eps;
- v3_scale(&force,&distance,d);
- v3_add(&(ai->f),&(ai->f),&force);
- }
+int moldyn_free_save_file(t_moldyn *moldyn) {
+
+ free(moldyn->atom);
+
+ return 0;
+}
+
+int moldyn_load(t_moldyn *moldyn) {
+
+ // later ...
return 0;
}
/*
- * tersoff potential & force for 2 sorts of atoms
+ * function to find/callback all combinations of 2 body bonds
*/
-/* create mixed terms from parameters and set them */
-int tersoff_mult_complete_params(t_tersoff_mult_params *p) {
-
- printf("[moldyn] tersoff parameter completion\n");
- p->Smixed=sqrt(p->S[0]*p->S[1]);
- p->Rmixed=sqrt(p->R[0]*p->R[1]);
- p->Amixed=sqrt(p->A[0]*p->A[1]);
- p->Bmixed=sqrt(p->B[0]*p->B[1]);
- p->lambda_m=0.5*(p->lambda[0]+p->lambda[1]);
- p->mu_m=0.5*(p->mu[0]+p->mu[1]);
-
- printf("[moldyn] tersoff mult parameter info:\n");
- printf(" S (m) | %.12f | %.12f | %.12f\n",p->S[0],p->S[1],p->Smixed);
- printf(" R (m) | %.12f | %.12f | %.12f\n",p->R[0],p->R[1],p->Rmixed);
- printf(" A (eV) | %f | %f | %f\n",p->A[0]/EV,p->A[1]/EV,p->Amixed/EV);
- printf(" B (eV) | %f | %f | %f\n",p->B[0]/EV,p->B[1]/EV,p->Bmixed/EV);
- printf(" lambda | %f | %f | %f\n",p->lambda[0],p->lambda[1],
- p->lambda_m);
- printf(" mu | %f | %f | %f\n",p->mu[0],p->mu[1],p->mu_m);
- printf(" beta | %.10f | %.10f\n",p->beta[0],p->beta[1]);
- printf(" n | %f | %f\n",p->n[0],p->n[1]);
- printf(" c | %f | %f\n",p->c[0],p->c[1]);
- printf(" d | %f | %f\n",p->d[0],p->d[1]);
- printf(" h | %f | %f\n",p->h[0],p->h[1]);
- printf(" chi | %f \n",p->chi);
+int process_2b_bonds(t_moldyn *moldyn,void *data,
+ int (*process)(t_moldyn *moldyn,t_atom *itom,t_atom *jtom,
+ void *data,u8 bc)) {
+
+ t_linkcell *lc;
+#ifdef STATIC_LISTS
+ int *neighbour[27];
+ int p;
+#else
+ t_list neighbour[27];
+#endif
+ u8 bc;
+ t_atom *itom,*jtom;
+ int i,j;
+ t_list *this;
+
+ lc=&(moldyn->lc);
+
+ link_cell_init(moldyn,VERBOSE);
+
+ itom=moldyn->atom;
+
+ for(i=0;i<moldyn->count;i++) {
+ /* neighbour indexing */
+ link_cell_neighbour_index(moldyn,
+ (itom[i].r.x+moldyn->dim.x/2)/lc->x,
+ (itom[i].r.y+moldyn->dim.y/2)/lc->x,
+ (itom[i].r.z+moldyn->dim.z/2)/lc->x,
+ neighbour);
+
+ for(j=0;j<27;j++) {
+
+ bc=(j<lc->dnlc)?0:1;
+
+#ifdef STATIC_LISTS
+ p=0;
+
+ while(neighbour[j][p]!=0) {
+
+ jtom=&(moldyn->atom[neighbour[j][p]]);
+ p++;
+#else
+ this=&(neighbour[j]);
+ list_reset_f(this);
+
+ if(this->start==NULL)
+ continue;
+
+ do {
+
+ jtom=this->current->data;
+#endif
+
+ /* process bond */
+ process(moldyn,&(itom[i]),jtom,data,bc);
+
+#ifdef STATIC_LISTS
+ }
+#else
+ } while(list_next_f(this)!=L_NO_NEXT_ELEMENT);
+#endif
+ }
+ }
return 0;
+
+}
+
+/*
+ * post processing functions
+ */
+
+int get_line(int fd,char *line,int max) {
+
+ int count,ret;
+
+ count=0;
+
+ while(1) {
+ if(count==max) return count;
+ ret=read(fd,line+count,1);
+ if(ret<=0) return ret;
+ if(line[count]=='\n') {
+ line[count]='\0';
+ return count+1;
+ }
+ count+=1;
+ }
}
-/* tersoff 1 body part */
-int tersoff_mult_1bp(t_moldyn *moldyn,t_atom *ai) {
+int pair_correlation_init(t_moldyn *moldyn,double dr) {
- int num;
- t_tersoff_mult_params *params;
- t_tersoff_exchange *exchange;
- num=ai->bnum;
- params=moldyn->pot1b_params;
- exchange=&(params->exchange);
+ return 0;
+}
- /*
- * simple: point constant parameters only depending on atom i to
- * their right values
- */
+int calculate_diffusion_coefficient(t_moldyn *moldyn,double *dc) {
+
+ int i;
+ t_atom *atom;
+ t_3dvec dist;
+ double d2;
+ int a_cnt;
+ int b_cnt;
- exchange->beta=&(params->beta[num]);
- exchange->n=&(params->n[num]);
- exchange->c=&(params->c[num]);
- exchange->d=&(params->d[num]);
- exchange->h=&(params->h[num]);
+ atom=moldyn->atom;
+ dc[0]=0;
+ dc[1]=0;
+ dc[2]=0;
+ a_cnt=0;
+ b_cnt=0;
+
+ for(i=0;i<moldyn->count;i++) {
- exchange->betan=pow(*(exchange->beta),*(exchange->n));
- exchange->n_betan=*(exchange->n)*exchange->betan;
- exchange->c2=params->c[num]*params->c[num];
- exchange->d2=params->d[num]*params->d[num];
- exchange->c2d2=exchange->c2/exchange->d2;
+ v3_sub(&dist,&(atom[i].r),&(atom[i].r_0));
+ check_per_bound(moldyn,&dist);
+ d2=v3_absolute_square(&dist);
+ if(atom[i].brand) {
+ b_cnt+=1;
+ dc[1]+=d2;
+ }
+ else {
+ a_cnt+=1;
+ dc[0]+=d2;
+ }
+
+ dc[2]+=d2;
+ }
+
+ dc[0]*=(1.0/(6.0*moldyn->time*a_cnt));
+ dc[1]*=(1.0/(6.0*moldyn->time*b_cnt));
+ dc[2]*=(1.0/(6.0*moldyn->time*moldyn->count));
+
return 0;
}
-
-/* tersoff 2 body part */
-int tersoff_mult_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
-
- t_tersoff_mult_params *params;
- t_tersoff_exchange *exchange;
- t_3dvec dist_ij,force;
- double d_ij;
- double A,B,R,S,lambda,mu;
- double f_r,df_r;
- double f_c,df_c;
- int num;
- double s_r;
- double arg;
- double scale;
- params=moldyn->pot2b_params;
- num=ai->bnum;
- exchange=&(params->exchange);
+int bonding_analyze(t_moldyn *moldyn,double *cnt) {
+
+ return 0;
+}
+
+int calculate_pair_correlation_process(t_moldyn *moldyn,t_atom *itom,
+ t_atom *jtom,void *data,u8 bc) {
+
+ t_3dvec dist;
+ double d;
+ int s;
+ t_pcc *pcc;
+
+ /* only count pairs once,
+ * skip same atoms */
+ if(itom->tag>=jtom->tag)
+ return 0;
- exchange->run3bp=0;
- exchange->run2bp_post=0;
-
/*
- * we need: f_c, df_c, f_r, df_r
- *
- * therefore we need: R, S, A, lambda
+ * pair correlation calc
*/
- v3_sub(&dist_ij,&(ai->r),&(aj->r));
+ /* get pcc data */
+ pcc=data;
- if(bc) check_per_bound(moldyn,&dist_ij);
+ /* distance */
+ v3_sub(&dist,&(jtom->r),&(itom->r));
+ if(bc) check_per_bound(moldyn,&dist);
+ d=v3_absolute_square(&dist);
- d_ij=v3_norm(&dist_ij);
+ /* ignore if greater cutoff */
+ if(d>moldyn->cutoff_square)
+ return 0;
- /* save for use in 3bp */
- exchange->d_ij=d_ij;
- exchange->dist_ij=dist_ij;
- exchange->d_ij2=d_ij*d_ij;
+ /* fill the slots */
+ d=sqrt(d);
+ s=(int)(d/pcc->dr);
+
+ /* should never happen but it does 8) -
+ * related to -ffloat-store problem! */
+ if(s>=pcc->o1) {
+ printf("[moldyn] WARNING: pcc (%d/%d)",
+ s,pcc->o1);
+ printf("\n");
+ s=pcc->o1-1;
+ }
- /* constants */
- if(num==aj->bnum) {
- S=params->S[num];
- R=params->R[num];
- A=params->A[num];
- B=params->B[num];
- lambda=params->lambda[num];
- mu=params->mu[num];
- params->exchange.chi=1.0;
+ if(itom->brand!=jtom->brand) {
+ /* mixed */
+ pcc->stat[s]+=1;
}
else {
- S=params->Smixed;
- R=params->Rmixed;
- A=params->Amixed;
- B=params->Bmixed;
- lambda=params->lambda_m;
- mu=params->mu_m;
- params->exchange.chi=params->chi;
+ /* type a - type a bonds */
+ if(itom->brand==0)
+ pcc->stat[s+pcc->o1]+=1;
+ else
+ /* type b - type b bonds */
+ pcc->stat[s+pcc->o2]+=1;
}
- if(d_ij>S)
- return 0;
+ return 0;
+}
- f_r=A*exp(-lambda*d_ij);
- df_r=-lambda*f_r/d_ij;
+int calculate_pair_correlation(t_moldyn *moldyn,double dr,void *ptr) {
- /* f_a, df_a calc + save for later use */
- exchange->f_a=-B*exp(-mu*d_ij);
- exchange->df_a=-mu*exchange->f_a/d_ij;
+ t_pcc pcc;
+ double norm;
+ int i;
+
+ pcc.dr=dr;
+ pcc.o1=moldyn->cutoff/dr;
+ pcc.o2=2*pcc.o1;
+
+ if(pcc.o1*dr<=moldyn->cutoff)
+ printf("[moldyn] WARNING: pcc (low #slots)\n");
+
+ printf("[moldyn] pair correlation calc info:\n");
+ printf(" time: %f\n",moldyn->time);
+ printf(" count: %d\n",moldyn->count);
+ printf(" cutoff: %f\n",moldyn->cutoff);
+ printf(" temperature: cur=%f avg=%f\n",moldyn->t,moldyn->t_avg);
- if(d_ij<R) {
- /* f_c = 1, df_c = 0 */
- f_c=1.0;
- df_c=0.0;
- v3_scale(&force,&dist_ij,df_r);
+ if(ptr!=NULL) {
+ pcc.stat=(double *)ptr;
}
else {
- s_r=S-R;
- arg=M_PI*(d_ij-R)/s_r;
- f_c=0.5+0.5*cos(arg);
- df_c=-0.5*sin(arg)*(M_PI/(s_r*d_ij));
- scale=df_c*f_r+df_r*f_c;
- v3_scale(&force,&dist_ij,scale);
+ pcc.stat=(double *)malloc(3*pcc.o1*sizeof(double));
+ if(pcc.stat==NULL) {
+ perror("[moldyn] pair correlation malloc");
+ return -1;
+ }
}
- /* add forces */
- v3_add(&(ai->f),&(ai->f),&force);
- /* energy is 0.5 f_r f_c ... */
- moldyn->energy+=(0.5*f_r*f_c);
+ memset(pcc.stat,0,3*pcc.o1*sizeof(double));
- /* save for use in 3bp */
- exchange->f_c=f_c;
- exchange->df_c=df_c;
+ /* process */
+ process_2b_bonds(moldyn,&pcc,calculate_pair_correlation_process);
- /* enable the run of 3bp function and 2bp post processing */
- exchange->run3bp=1;
- exchange->run2bp_post=1;
+ /* normalization */
+ for(i=1;i<pcc.o1;i++) {
+ // normalization: 4 pi r^2 dr
+ // here: not double counting pairs -> 2 pi r r dr
+ // ... and actually it's a constant times r^2
+ norm=i*i*dr*dr;
+ pcc.stat[i]/=norm;
+ pcc.stat[pcc.o1+i]/=norm;
+ pcc.stat[pcc.o2+i]/=norm;
+ }
+ /* */
- /* reset 3bp sums */
- exchange->sum1_3bp=0.0;
- exchange->sum2_3bp=0.0;
- v3_zero(&(exchange->db_ij));
+ if(ptr==NULL) {
+ /* todo: store/print pair correlation function */
+ free(pcc.stat);
+ }
return 0;
}
-/* tersoff 2 body post part */
+int bond_analyze_process(t_moldyn *moldyn,t_atom *itom,t_atom *jtom,
+ void *data,u8 bc) {
-int tersoff_mult_post_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
-
- /* here we have to allow for the 3bp sums */
-
- t_tersoff_mult_params *params;
- t_tersoff_exchange *exchange;
-
- t_3dvec force,temp,*db_ij,*dist_ij;
- double db_ij_scale1,db_ij_scale2;
- double b_ij;
- double f_c,df_c,f_a,df_a;
- double chi,betan;
- double help;
- double n;
-
- params=moldyn->pot2b_params;
- exchange=&(params->exchange);
+ t_ba *ba;
+ t_3dvec dist;
+ double d;
- /* we do not run if f_c_ij was dtected to be 0! */
- if(!(exchange->run2bp_post))
+ if(itom->tag>=jtom->tag)
return 0;
- db_ij=&(exchange->db_ij);
- f_c=exchange->f_c;
- df_c=exchange->df_c;
- f_a=exchange->f_a;
- df_a=exchange->df_a;
- betan=exchange->betan;
- n=*(exchange->n);
- chi=exchange->chi;
- dist_ij=&(exchange->dist_ij);
+ /* distance */
+ v3_sub(&dist,&(jtom->r),&(itom->r));
+ if(bc) check_per_bound(moldyn,&dist);
+ d=v3_absolute_square(&dist);
- db_ij_scale1=(1+betan*exchange->sum1_3bp);
- db_ij_scale2=(exchange->n_betan*exchange->sum2_3bp);
- help=pow(db_ij_scale1,-1.0/(2*n)-1);
- b_ij=chi*db_ij_scale1*help;
- db_ij_scale1=-chi/(2*n)*help;
-
- /* db_ij part */
- v3_scale(db_ij,db_ij,(db_ij_scale1*db_ij_scale2));
- v3_scale(db_ij,db_ij,f_a);
+ /* ignore if greater or equal cutoff */
+ if(d>moldyn->cutoff_square)
+ return 0;
- /* df_a part */
- v3_scale(&temp,dist_ij,b_ij*df_a);
+ /* check for potential bond */
+ if(moldyn->check_2b_bond(moldyn,itom,jtom,bc)==FALSE)
+ return 0;
- /* db_ij + df_a part */
- v3_add(&force,&temp,db_ij);
- v3_scale(&force,&force,f_c);
+ d=sqrt(d);
- /* df_c part */
- v3_scale(&temp,dist_ij,f_a*b_ij*df_c);
+ /* now count this bonding ... */
+ ba=data;
- /* add energy of 3bp sum */
- moldyn->energy+=(0.5*f_c*b_ij*f_a);
+ /* increase total bond counter
+ * ... double counting!
+ */
+ ba->tcnt+=2;
- /* add force of 3bp calculation (all three parts) */
- v3_add(&(ai->f),&temp,&force);
+ if(itom->brand==0)
+ ba->acnt[jtom->tag]+=1;
+ else
+ ba->bcnt[jtom->tag]+=1;
+
+ if(jtom->brand==0)
+ ba->acnt[itom->tag]+=1;
+ else
+ ba->bcnt[itom->tag]+=1;
return 0;
}
-/* tersoff 3 body part */
-
-int tersoff_mult_3bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,t_atom *ak,u8 bc) {
-
- t_tersoff_mult_params *params;
- t_tersoff_exchange *exchange;
- t_3dvec dist_ij,dist_ik,dist_jk;
- t_3dvec temp,force;
- double R,S,s_r;
- double d_ij,d_ij2,d_ik,d_jk;
- double f_c,df_c,f_a,df_a;
- double f_c_ik,df_c_ik,arg;
- double n,c,d,h;
- double c2,d2,c2d2;
- double numer,denom;
- double theta,cos_theta,sin_theta;
- double d_theta,d_theta1,d_theta2;
- double h_cos,d2_h_cos2;
- double frac,bracket,bracket_n_1,bracket_n;
- double g;
- int num;
-
- params=moldyn->pot3b_params;
- num=ai->bnum;
- exchange=&(params->exchange);
-
- if(!(exchange->run3bp))
- return 0;
+int bond_analyze(t_moldyn *moldyn,double *quality) {
- /*
- * we need: f_c, d_fc, b_ij, db_ij, f_a, df_a
- *
- * we got f_c, df_c, f_a, df_a from 2bp calculation
- */
+ // by now: # bonds of type 'a-4b' and 'b-4a' / # bonds total
- d_ij=exchange->d_ij;
- d_ij2=exchange->d_ij2;
- dist_ij=exchange->dist_ij;
+ int qcnt;
+ int ccnt,cset;
+ t_ba ba;
+ int i;
+ t_atom *atom;
- f_a=params->exchange.f_a;
- df_a=params->exchange.df_a;
+ ba.acnt=malloc(moldyn->count*sizeof(int));
+ if(ba.acnt==NULL) {
+ perror("[moldyn] bond analyze malloc (a)");
+ return -1;
+ }
+ memset(ba.acnt,0,moldyn->count*sizeof(int));
- f_c=exchange->f_c;
- df_c=exchange->df_c;
-
- /* d_ij is <= S, as we didn't return so far! */
+ ba.bcnt=malloc(moldyn->count*sizeof(int));
+ if(ba.bcnt==NULL) {
+ perror("[moldyn] bond analyze malloc (b)");
+ return -1;
+ }
+ memset(ba.bcnt,0,moldyn->count*sizeof(int));
- /*
- * calc of b_ij (scalar) and db_ij (vector)
- *
- * - for b_ij: chi, beta, f_c_ik, w(=1), c, d, h, n, cos_theta
- *
- * - for db_ij: d_theta, sin_theta, cos_theta, f_c_ik, df_c_ik,
- * w_ik,
- *
- */
+ ba.tcnt=0;
+ qcnt=0;
+ ccnt=0;
+ cset=0;
- v3_sub(&dist_ik,&(ai->r),&(ak->r));
- if(bc) check_per_bound(moldyn,&dist_ik);
- d_ik=v3_norm(&dist_ik);
+ atom=moldyn->atom;
- /* constants for f_c_ik calc */
- if(num==ak->bnum) {
- R=params->R[num];
- S=params->S[num];
- }
- else {
- R=params->Rmixed;
- S=params->Smixed;
- }
+ process_2b_bonds(moldyn,&ba,bond_analyze_process);
- /* calc of f_c_ik */
- if(d_ik>S) {
- f_c_ik=0.0;
- df_c_ik=0.0;
+ for(i=0;i<moldyn->count;i++) {
+ if(atom[i].brand==0) {
+ if((ba.acnt[i]==0)&(ba.bcnt[i]==4))
+ qcnt+=4;
+ }
+ else {
+ if((ba.acnt[i]==4)&(ba.bcnt[i]==0)) {
+ qcnt+=4;
+ ccnt+=1;
+ }
+ cset+=1;
+ }
}
- else if(d_ik<R) {
- f_c_ik=1.0;
- df_c_ik=0.0;
+
+ printf("[moldyn] bond analyze: c_cnt=%d | set=%d\n",ccnt,cset);
+ printf("[moldyn] bond analyze: q_cnt=%d | tot=%d\n",qcnt,ba.tcnt);
+
+ if(quality) {
+ quality[0]=1.0*ccnt/cset;
+ quality[1]=1.0*qcnt/ba.tcnt;
}
else {
- s_r=S-R;
- arg=M_PI*(d_ik-R)/s_r;
- f_c_ik=0.5+0.5*cos(arg);
- df_c_ik=-0.5*sin(arg)*(M_PI/(s_r*d_ik));
+ printf("[moldyn] bond analyze: c_bnd_q=%f\n",1.0*qcnt/ba.tcnt);
+ printf("[moldyn] bond analyze: tot_q=%f\n",1.0*qcnt/ba.tcnt);
}
-
- v3_sub(&dist_jk,&(aj->r),&(ak->r));
- if(bc) check_per_bound(moldyn,&dist_jk);
- d_jk=v3_norm(&dist_jk);
-
- /* get exchange data */
- n=*(exchange->n);
- c=*(exchange->c);
- d=*(exchange->d);
- h=*(exchange->h);
- c2=exchange->c2;
- d2=exchange->d2;
- c2d2=exchange->c2d2;
-
- numer=d_ij2+d_ik*d_ik-d_jk*d_jk;
- denom=2*d_ij*d_ik;
- cos_theta=numer/denom;
- /* prefere law of cosines, dot product -> nan (often) */
- //cos_theta=v3_scalar_product(&dist_ij,&dist_ik)/(d_ij*d_ik);
- sin_theta=sqrt(1.0-(cos_theta*cos_theta));
- theta=acos(cos_theta);
- d_theta=(-1.0/sqrt(1.0-cos_theta*cos_theta))/(denom*denom);
- d_theta1=2*denom-numer*2*d_ik/d_ij;
- d_theta2=2*denom-numer*2*d_ij/d_ik;
- d_theta1*=d_theta;
- d_theta2*=d_theta;
-
- h_cos=(h-cos_theta);
- d2_h_cos2=d2+(h_cos*h_cos);
-
- frac=c2/(d2_h_cos2);
- g=1.0+c2d2-frac;
-
- if(f_c_ik==0.0) {
- bracket=0.0;
- bracket_n_1=0.0;
- bracket_n=0.0;
- //printf("Foo -> 0: ");
- }
- else {
- bracket=f_c_ik*g;
- bracket_n_1=pow(bracket,n-1.0);
- bracket_n=bracket_n_1*bracket;
- //printf("Foo -> 1: ");
+
+ return 0;
+}
+
+/*
+ * visualization code
+ */
+
+int visual_init(t_moldyn *moldyn,char *filebase) {
+
+ strncpy(moldyn->vis.fb,filebase,128);
+
+ return 0;
+}
+
+int visual_atoms(t_moldyn *moldyn) {
+
+ int i,j,fd;
+ char file[128+64];
+ t_3dvec dim;
+ double help;
+ t_visual *v;
+ t_atom *atom;
+ t_atom *btom;
+ t_linkcell *lc;
+#ifdef STATIC_LISTS
+ int *neighbour[27];
+ int p;
+#else
+ t_list neighbour[27];
+#endif
+ u8 bc;
+ t_3dvec dist;
+ double d2;
+ u8 brand;
+
+ v=&(moldyn->vis);
+ dim.x=v->dim.x;
+ dim.y=v->dim.y;
+ dim.z=v->dim.z;
+ atom=moldyn->atom;
+ lc=&(moldyn->lc);
+
+ help=(dim.x+dim.y);
+
+ sprintf(file,"%s/atomic_conf_%07.f.xyz",v->fb,moldyn->time);
+ fd=open(file,O_WRONLY|O_CREAT|O_TRUNC,S_IRUSR|S_IWUSR);
+ if(fd<0) {
+ perror("open visual save file fd");
+ return -1;
}
-//printf("%.15f %.15f %.15f\n",bracket_n_1,bracket_n,bracket);
- /* calc of db_ij and the 2 sums */
- exchange->sum1_3bp+=bracket_n;
- exchange->sum2_3bp+=bracket_n_1;
+ /* write the actual data file */
- /* derivation of theta */
- v3_scale(&force,&dist_ij,d_theta1);
- v3_scale(&temp,&dist_ik,d_theta2);
- v3_add(&force,&force,&temp);
+ // povray header
+ dprintf(fd,"# [P] %d %07.f <%f,%f,%f>\n",
+ moldyn->count,moldyn->time,help/40.0,help/40.0,-0.8*help);
- /* part 1 of db_ij */
- v3_scale(&force,&force,sin_theta*2*h_cos*f_c_ik*frac/d2_h_cos2);
+ // atomic configuration
+ for(i=0;i<moldyn->count;i++) {
+ // atom type, positions, color and kinetic energy
+ dprintf(fd,"%s %f %f %f %s %f\n",pse_name[atom[i].element],
+ atom[i].r.x,
+ atom[i].r.y,
+ atom[i].r.z,
+ pse_col[atom[i].element],
+ atom[i].ekin);
+
+ /*
+ * bond detection should usually be done by potential
+ * functions. brrrrr! EVIL!
+ *
+ * todo: potentials need to export a 'find_bonds' function!
+ */
+
+ // bonds between atoms
+ if(!(atom[i].attr&ATOM_ATTR_VB))
+ continue;
+ link_cell_neighbour_index(moldyn,
+ (atom[i].r.x+moldyn->dim.x/2)/lc->x,
+ (atom[i].r.y+moldyn->dim.y/2)/lc->y,
+ (atom[i].r.z+moldyn->dim.z/2)/lc->z,
+ neighbour);
+ for(j=0;j<27;j++) {
+ bc=j<lc->dnlc?0:1;
+#ifdef STATIC_LISTS
+ p=0;
+ while(neighbour[j][p]!=0) {
+ btom=&(atom[neighbour[j][p]]);
+ p++;
+#else
+ list_reset_f(&neighbour[j]);
+ if(neighbour[j].start==NULL)
+ continue;
+ do {
+ btom=neighbour[j].current->data;
+#endif
+ if(btom==&atom[i]) // skip identical atoms
+ continue;
+ //if(btom<&atom[i]) // skip half of them
+ // continue;
+ v3_sub(&dist,&(atom[i].r),&(btom->r));
+ if(bc) check_per_bound(moldyn,&dist);
+ d2=v3_absolute_square(&dist);
+ brand=atom[i].brand;
+ if(brand==btom->brand) {
+ if(d2>moldyn->bondlen[brand])
+ continue;
+ }
+ else {
+ if(d2>moldyn->bondlen[2])
+ continue;
+ }
+ dprintf(fd,"# [B] %f %f %f %f %f %f\n",
+ atom[i].r.x,atom[i].r.y,atom[i].r.z,
+ btom->r.x,btom->r.y,btom->r.z);
+#ifdef STATIC_LISTS
+ }
+#else
+ } while(list_next_f(&neighbour[j])!=L_NO_NEXT_ELEMENT);
+#endif
+ }
+ }
- /* part 2 of db_ij */
- v3_scale(&temp,&dist_ik,df_c_ik*g);
+ // boundaries
+ if(dim.x) {
+ dprintf(fd,"# [D] %f %f %f %f %f %f\n",
+ -dim.x/2,-dim.y/2,-dim.z/2,
+ dim.x/2,-dim.y/2,-dim.z/2);
+ dprintf(fd,"# [D] %f %f %f %f %f %f\n",
+ -dim.x/2,-dim.y/2,-dim.z/2,
+ -dim.x/2,dim.y/2,-dim.z/2);
+ dprintf(fd,"# [D] %f %f %f %f %f %f\n",
+ dim.x/2,dim.y/2,-dim.z/2,
+ dim.x/2,-dim.y/2,-dim.z/2);
+ dprintf(fd,"# [D] %f %f %f %f %f %f\n",
+ -dim.x/2,dim.y/2,-dim.z/2,
+ dim.x/2,dim.y/2,-dim.z/2);
+
+ dprintf(fd,"# [D] %f %f %f %f %f %f\n",
+ -dim.x/2,-dim.y/2,dim.z/2,
+ dim.x/2,-dim.y/2,dim.z/2);
+ dprintf(fd,"# [D] %f %f %f %f %f %f\n",
+ -dim.x/2,-dim.y/2,dim.z/2,
+ -dim.x/2,dim.y/2,dim.z/2);
+ dprintf(fd,"# [D] %f %f %f %f %f %f\n",
+ dim.x/2,dim.y/2,dim.z/2,
+ dim.x/2,-dim.y/2,dim.z/2);
+ dprintf(fd,"# [D] %f %f %f %f %f %f\n",
+ -dim.x/2,dim.y/2,dim.z/2,
+ dim.x/2,dim.y/2,dim.z/2);
+
+ dprintf(fd,"# [D] %f %f %f %f %f %f\n",
+ -dim.x/2,-dim.y/2,dim.z/2,
+ -dim.x/2,-dim.y/2,-dim.z/2);
+ dprintf(fd,"# [D] %f %f %f %f %f %f\n",
+ -dim.x/2,dim.y/2,dim.z/2,
+ -dim.x/2,dim.y/2,-dim.z/2);
+ dprintf(fd,"# [D] %f %f %f %f %f %f\n",
+ dim.x/2,-dim.y/2,dim.z/2,
+ dim.x/2,-dim.y/2,-dim.z/2);
+ dprintf(fd,"# [D] %f %f %f %f %f %f\n",
+ dim.x/2,dim.y/2,dim.z/2,
+ dim.x/2,dim.y/2,-dim.z/2);
+ }
+
+ close(fd);
- /* sum up and add to db_ij */
- v3_add(&temp,&temp,&force);
- v3_add(&(exchange->db_ij),&(exchange->db_ij),&temp);
-
return 0;
}