#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"
+/*
+ * 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 moldyn_init(t_moldyn *moldyn,int argc,char **argv) {
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;
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;
+}
+
int set_temperature(t_moldyn *moldyn,double t_ref) {
moldyn->t_ref=t_ref;
moldyn->p_ref=p_ref;
- printf("[moldyn] pressure [atm]: %f\n",moldyn->p_ref/ATM);
+ printf("[moldyn] pressure [bar]: %f\n",moldyn->p_ref/BAR);
return 0;
}
return 0;
}
-int set_potential2b_post(t_moldyn *moldyn,pf_func2b_post func) {
+int set_potential3b_j1(t_moldyn *moldyn,pf_func2b func) {
+
+ moldyn->func3b_j1=func;
+
+ return 0;
+}
+
+int set_potential3b_j2(t_moldyn *moldyn,pf_func2b func) {
+
+ moldyn->func3b_j2=func;
+
+ return 0;
+}
+
+int set_potential3b_j3(t_moldyn *moldyn,pf_func2b func) {
+
+ moldyn->func3b_j3=func;
+
+ return 0;
+}
+
+int set_potential3b_k1(t_moldyn *moldyn,pf_func3b func) {
- moldyn->func2b_post=func;
+ moldyn->func3b_k1=func;
return 0;
}
-int set_potential3b(t_moldyn *moldyn,pf_func3b func) {
+int set_potential3b_k2(t_moldyn *moldyn,pf_func3b func) {
- moldyn->func3b=func;
+ moldyn->func3b_k2=func;
return 0;
}
return 0;
}
+int set_avg_skip(t_moldyn *moldyn,int skip) {
+
+ printf("[moldyn] skip %d steps before starting average calc\n",skip);
+ moldyn->avg_skip=skip;
+
+ return 0;
+}
+
int moldyn_set_log_dir(t_moldyn *moldyn,char *dir) {
strncpy(moldyn->vlsdir,dir,127);
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 SAVE_STEP:
moldyn->swrite=timer;
printf("save file (%d)\n",timer);
break;
case VISUAL_STEP:
moldyn->vwrite=timer;
- ret=visual_init(&(moldyn->vis),moldyn->vlsdir);
+ ret=visual_init(moldyn,moldyn->vlsdir);
if(ret<0) {
printf("[moldyn] visual init failure\n");
return ret;
perror("[moldyn] report fd open");
return moldyn->rfd;
}
- snprintf(filename,127,"%s/plot.scr",moldyn->vlsdir);
- moldyn->pfd=open(filename,
- O_WRONLY|O_CREAT|O_EXCL,
- S_IRUSR|S_IWUSR);
- if(moldyn->pfd<0) {
- perror("[moldyn] plot fd open");
- return moldyn->pfd;
+ 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);
- dprintf(moldyn->pfd,plot_script);
- close(moldyn->pfd);
+ printf("\n");
break;
default:
printf("unknown log type: %02x\n",type);
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->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 && gnuplot plot.scr",moldyn->vlsdir);
- system(sc);
- snprintf(sc,255,"cd %s && pdflatex report",moldyn->vlsdir);
+ snprintf(sc,255,"cd %s && pdflatex report >/dev/null 2>&1",
+ moldyn->vlsdir);
system(sc);
- snprintf(sc,255,"cd %s && pdflatex report",moldyn->vlsdir);
+ snprintf(sc,255,"cd %s && pdflatex report >/dev/null 2>&1",
+ moldyn->vlsdir);
system(sc);
- snprintf(sc,255,"cd %s && dvipdf report",moldyn->vlsdir);
+ snprintf(sc,255,"cd %s && dvipdf report >/dev/null 2>&1",
+ moldyn->vlsdir);
system(sc);
}
- if(&(moldyn->vis)) visual_tini(&(moldyn->vis));
return 0;
}
*/
int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass,
- u8 attr,u8 brand,int a,int b,int c) {
+ u8 attr,u8 brand,int a,int b,int c,t_3dvec *origin) {
int new,count;
int ret;
- t_3dvec origin;
+ t_3dvec orig;
void *ptr;
t_atom *atom;
atom=&(moldyn->atom[count]);
/* no atoms on the boundaries (only reason: it looks better!) */
- origin.x=0.5*lc;
- origin.y=0.5*lc;
- origin.z=0.5*lc;
+ 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,&origin);
+ ret=cubic_init(a,b,c,lc,atom,&orig);
break;
case FCC:
- v3_scale(&origin,&origin,0.5);
+ 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,&origin);
+ ret=fcc_init(a,b,c,lc,atom,&orig);
break;
case DIAMOND:
- v3_scale(&origin,&origin,0.25);
+ 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,&origin);
+ ret=diamond_init(a,b,c,lc,atom,&orig);
break;
default:
printf("unknown lattice type (%02x)\n",type);
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 brand,u8 attr,
+ t_3dvec *r,t_3dvec *v) {
+
+ t_atom *atom;
+ void *ptr;
+ int count;
+
+ atom=moldyn->atom;
+ count=(moldyn->count)++;
+
+ 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].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) {
return count;
}
-int add_atom(t_moldyn *moldyn,int element,double mass,u8 brand,u8 attr,
- t_3dvec *r,t_3dvec *v) {
-
- t_atom *atom;
- void *ptr;
- int count;
-
- atom=moldyn->atom;
- count=(moldyn->count)++;
-
- 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].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;
-
- return 0;
-}
-
int destroy_atoms(t_moldyn *moldyn) {
if(moldyn->atom) free(moldyn->atom);
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 */
return p;
}
-double pressure_calc(t_moldyn *moldyn) {
+double virial_sum(t_moldyn *moldyn) {
int i;
double v;
t_virial *virial;
- /*
- * P = 1/(3V) sum_i ( p_i^2 / 2m + f_i r_i )
- *
- * virial = f_i r_i
- */
-
+ /* virial (sum over atom virials) */
v=0.0;
for(i=0;i<moldyn->count;i++) {
virial=&(moldyn->atom[i].virial);
v+=(virial->xx+virial->yy+virial->zz);
}
+ moldyn->virial=v;
+
+ /* global virial (absolute coordinates) */
+ virial=&(moldyn->gvir);
+ moldyn->gv=virial->xx+virial->yy+virial->zz;
+
+ return moldyn->virial;
+}
+
+double pressure_calc(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)
+ */
- /* assume up to date kinetic energy */
- moldyn->p=2.0*moldyn->ekin+v;
+ /* assume up to date virial & up to date kinetic energy */
+
+ /* pressure (atom virials) */
+ moldyn->p=2.0*moldyn->ekin+moldyn->virial;
moldyn->p/=(3.0*moldyn->volume);
+ /* pressure (absolute coordinates) */
+ moldyn->gp=2.0*moldyn->ekin+moldyn->gv;
+ moldyn->gp/=(3.0*moldyn->volume);
+
return moldyn->p;
-}
+}
+
+int average_and_fluctuation_calc(t_moldyn *moldyn) {
+
+ int denom;
+
+ if(moldyn->total_steps<moldyn->avg_skip)
+ return 0;
+
+ 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;
+
+ return 0;
+}
+
+int get_heat_capacity(t_moldyn *moldyn) {
+
+ double temp2,ighc;
+
+ /* averages needed for heat capacity calc */
+ if(moldyn->total_steps<moldyn->avg_skip)
+ return 0;
+
+ /* (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);
+
+ /* 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)));
+
+ return 0;
+}
double thermodynamic_pressure_calc(t_moldyn *moldyn) {
- t_3dvec dim,*tp;
- double u,p;
- double scale;
+ t_3dvec dim;
+ //t_3dvec *tp;
+ double u_up,u_down,dv;
+ double scale,p;
t_atom *store;
- tp=&(moldyn->tp);
+ /*
+ * dU = - p dV
+ *
+ * => p = - dU/dV
+ *
+ */
+
+ scale=0.00001;
+ dv=8*scale*scale*scale*moldyn->volume;
+
store=malloc(moldyn->count*sizeof(t_atom));
if(store==NULL) {
printf("[moldyn] allocating store mem failed\n");
}
/* save unscaled potential energy + atom/dim configuration */
- u=moldyn->energy;
memcpy(store,moldyn->atom,moldyn->count*sizeof(t_atom));
dim=moldyn->dim;
- /* derivative with respect to x direction */
- scale=1.0+moldyn->dv/(moldyn->dim.y*moldyn->dim.z);
- scale_dim(moldyn,scale,TRUE,0,0);
- scale_atoms(moldyn,scale,TRUE,0,0);
- link_cell_shutdown(moldyn);
- link_cell_init(moldyn,QUIET);
- potential_force_calc(moldyn);
- tp->x=(moldyn->energy-u)/moldyn->dv;
- p=tp->x*tp->x;
-
- /* restore atomic configuration + dim */
- memcpy(moldyn->atom,store,moldyn->count*sizeof(t_atom));
- moldyn->dim=dim;
-
- /* derivative with respect to y direction */
- scale=1.0+moldyn->dv/(moldyn->dim.x*moldyn->dim.z);
- scale_dim(moldyn,scale,0,TRUE,0);
- scale_atoms(moldyn,scale,0,TRUE,0);
- link_cell_shutdown(moldyn);
- link_cell_init(moldyn,QUIET);
- potential_force_calc(moldyn);
- tp->y=(moldyn->energy-u)/moldyn->dv;
- p+=tp->y*tp->y;
-
- /* restore atomic configuration + dim */
- memcpy(moldyn->atom,store,moldyn->count*sizeof(t_atom));
- moldyn->dim=dim;
-
- /* derivative with respect to z direction */
- scale=1.0+moldyn->dv/(moldyn->dim.x*moldyn->dim.y);
- scale_dim(moldyn,scale,0,0,TRUE);
- scale_atoms(moldyn,scale,0,0,TRUE);
+ /* scale up dimension and atom positions */
+ scale_dim(moldyn,SCALE_UP,scale,TRUE,TRUE,TRUE);
+ scale_atoms(moldyn,SCALE_UP,scale,TRUE,TRUE,TRUE);
link_cell_shutdown(moldyn);
link_cell_init(moldyn,QUIET);
potential_force_calc(moldyn);
- tp->z=(moldyn->energy-u)/moldyn->dv;
- p+=tp->z*tp->z;
+ u_up=moldyn->energy;
/* restore atomic configuration + dim */
memcpy(moldyn->atom,store,moldyn->count*sizeof(t_atom));
moldyn->dim=dim;
- printf("dU/dV komp addiert = %f %f %f\n",tp->x,tp->y,tp->z);
-
- scale=1.0+pow(moldyn->dv/moldyn->volume,ONE_THIRD);
-
-printf("debug: %f %f\n",moldyn->atom[0].r.x,moldyn->dim.x);
- scale_dim(moldyn,scale,1,1,1);
- scale_atoms(moldyn,scale,1,1,1);
+ /* scale down dimension and atom positions */
+ scale_dim(moldyn,SCALE_DOWN,scale,TRUE,TRUE,TRUE);
+ scale_atoms(moldyn,SCALE_DOWN,scale,TRUE,TRUE,TRUE);
link_cell_shutdown(moldyn);
link_cell_init(moldyn,QUIET);
potential_force_calc(moldyn);
-printf("debug: %f %f\n",moldyn->atom[0].r.x,moldyn->dim.x);
-
- printf("dU/dV einfach = %f\n",((moldyn->energy-u)/moldyn->dv)/ATM);
+ u_down=moldyn->energy;
+
+ /* calculate pressure */
+ p=-(u_up-u_down)/dv;
+printf("-------> %.10f %.10f %f\n",u_up/EV/moldyn->count,u_down/EV/moldyn->count,p/BAR);
/* restore atomic configuration + dim */
memcpy(moldyn->atom,store,moldyn->count*sizeof(t_atom));
moldyn->dim=dim;
/* restore energy */
- moldyn->energy=u;
+ potential_force_calc(moldyn);
link_cell_shutdown(moldyn);
link_cell_init(moldyn,QUIET);
- return sqrt(p);
+ return p;
}
double get_pressure(t_moldyn *moldyn) {
}
-int scale_dim(t_moldyn *moldyn,double scale,u8 x,u8 y,u8 z) {
+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,double scale,u8 x,u8 y,u8 z) {
+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;
moldyn->debug=scale;
/* scale the atoms and dimensions */
- scale_atoms(moldyn,scale,TRUE,TRUE,TRUE);
- scale_dim(moldyn,scale,TRUE,TRUE,TRUE);
+ scale_atoms(moldyn,SCALE_DIRECT,scale,TRUE,TRUE,TRUE);
+ scale_dim(moldyn,SCALE_DIRECT,scale,TRUE,TRUE,TRUE);
/* visualize dimensions */
if(vdim->x!=0) {
}
-double get_e_kin(t_moldyn *moldyn) {
+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++)
- moldyn->ekin+=0.5*atom[i].mass*v3_absolute_square(&(atom[i].v));
+ 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 update_e_kin(t_moldyn *moldyn) {
-
- return(get_e_kin(moldyn));
-}
-
double get_total_energy(t_moldyn *moldyn) {
return(moldyn->ekin+moldyn->energy);
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) printf("[moldyn] initializing linked cells (%d)\n",lc->cells);
+ 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);
- link_cell_update(moldyn);
-
return 0;
}
int nx,ny;
t_atom *atom;
t_linkcell *lc;
- double x,y,z;
+#ifdef STATIC_LISTS
+ int p;
+#endif
atom=moldyn->atom;
lc=&(moldyn->lc);
nx=lc->nx;
ny=lc->ny;
- x=moldyn->dim.x/2;
- y=moldyn->dim.y/2;
- z=moldyn->dim.z/2;
-
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);
- list_add_immediate_f(&(moldyn->lc.subcell[i+j*nx+k*nx*ny]),
+
+#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,t_list *cell) {
+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;
lc=&(moldyn->lc);
- for(i=0;i<lc->nx*lc->ny*lc->nz;i++)
- list_destroy_f(&(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);
int moldyn_integrate(t_moldyn *moldyn) {
int i;
- unsigned int e,m,s,v;
- t_3dvec p;
+ unsigned int e,m,s,v,p,t;
+ t_3dvec momentum;
t_moldyn_schedule *sched;
t_atom *atom;
int fd;
char dir[128];
double ds;
double energy_scale;
+ struct timeval t1,t2;
+ //double tp;
sched=&(moldyn->schedule);
atom=moldyn->atom;
m=moldyn->mwrite;
s=moldyn->swrite;
v=moldyn->vwrite;
+ p=moldyn->pwrite;
+ t=moldyn->twrite;
/* sqaure of some variables */
moldyn->tau_square=moldyn->tau*moldyn->tau;
moldyn->cutoff_square=moldyn->cutoff*moldyn->cutoff;
- /* energy scaling factor */
- energy_scale=moldyn->count*EV;
+ /* get current time */
+ gettimeofday(&t1,NULL);
/* calculate initial forces */
potential_force_calc(moldyn);
+#ifdef DEBUG
+//return 0;
+#endif
/* some stupid checks before we actually start calculating bullshit */
if(moldyn->cutoff>0.5*moldyn->dim.x)
/* zero absolute time */
moldyn->time=0.0;
+ moldyn->total_steps=0;
/* debugging, ignore */
moldyn->debug=0;
printf("[moldyn] integration start, go get a coffee ...\n");
/* executing the schedule */
- for(sched->count=0;sched->count<sched->total_sched;sched->count++) {
+ sched->count=0;
+ while(sched->count<sched->total_sched) {
/* setting amount of runs and finite time step size */
moldyn->tau=sched->tau[sched->count];
moldyn->tau_square=moldyn->tau*moldyn->tau;
moldyn->time_steps=sched->runs[sched->count];
+ /* energy scaling factor (might change!) */
+ energy_scale=moldyn->count*EV;
+
/* integration according to schedule */
for(i=0;i<moldyn->time_steps;i++) {
moldyn->integrate(moldyn);
/* calculate kinetic energy, temperature and pressure */
- update_e_kin(moldyn);
+ e_kin_calc(moldyn);
temperature_calc(moldyn);
+ virial_sum(moldyn);
pressure_calc(moldyn);
- //thermodynamic_pressure_calc(moldyn);
+ average_and_fluctuation_calc(moldyn);
/* p/t scaling */
if(moldyn->pt_scale&(T_SCALE_BERENDSEN|T_SCALE_DIRECT))
/* check for log & visualization */
if(e) {
- if(!(i%e))
+ if(!(moldyn->total_steps%e))
dprintf(moldyn->efd,
"%f %f %f %f\n",
moldyn->time,moldyn->ekin/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,
- "%f %f\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\n",moldyn->time,
+ moldyn->p/BAR,moldyn->p_avg/BAR,
+ moldyn->gp/BAR,moldyn->gp_avg/BAR);
+ }
+ }
+ if(t) {
+ if(!(moldyn->total_steps%t)) {
+ dprintf(moldyn->tfd,
+ "%f %f %f\n",
+ moldyn->time,moldyn->t,moldyn->t_avg);
}
}
if(s) {
- if(!(i%s)) {
+ 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);
+ 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));
}
}
if(v) {
- if(!(i%v)) {
- visual_atoms(&(moldyn->vis),moldyn->time,
- moldyn->atom,moldyn->count);
- printf("\rsched: %d, steps: %d, T: %f, P: %f V: %f",
- sched->count,i,
- moldyn->t,moldyn->p/ATM,moldyn->volume);
- fflush(stdout);
+ if(!(moldyn->total_steps%v)) {
+ visual_atoms(moldyn);
}
}
+ /* display progress */
+ //if(!(moldyn->total_steps%10)) {
+ /* get current time */
+ gettimeofday(&t2,NULL);
+
+printf("\rsched:%d, steps:%d/%d, T:%3.1f/%3.1f P:%4.1f/%4.1f V:%6.1f (%d)",
+ sched->count,i,moldyn->total_steps,
+ moldyn->t,moldyn->t_avg,
+ moldyn->p_avg/BAR,moldyn->gp_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(sched->hook)
+ if(sched->hook) {
+ printf("\n ## schedule hook %d start ##\n",
+ sched->count);
sched->hook(moldyn,sched->hook_params);
+ printf(" ## schedule hook end ##\n");
+ }
- /* get a new info line */
- printf("\n");
+ /* increase the schedule counter */
+ sched->count+=1;
}
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 *this,*that;
+#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++) {
}
- /* get energy,force and virial of every atom */
+ /* 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;
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;
+
+ while(neighbour_i[j][p]!=0) {
+
+ 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_f(this);
+
+ if(this->start==NULL)
+ continue;
+
+ do {
+ jtom=this->current->data;
+
+ 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);
+ }
+ } while(list_next_f(this)!=L_NO_NEXT_ELEMENT);
+#endif
+
+ }
+ }
+
+ /* 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;
- bc_ij=(j<dnlc)?0:1;
-
do {
+
jtom=this->current->data;
+#endif
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);
- }
+ if(!(jtom->attr&ATOM_ATTR_3BP))
+ continue;
- /* 3 body potential/force */
+ /* reset 3bp run */
+ moldyn->run3bp=1;
- if(!(itom[i].attr&ATOM_ATTR_3BP)||
- !(jtom->attr&ATOM_ATTR_3BP))
- continue;
+ if(moldyn->func3b_j1)
+ moldyn->func3b_j1(moldyn,
+ &(itom[i]),
+ jtom,
+ bc_ij);
- /* copy the neighbour lists */
- memcpy(neighbour_i2,neighbour_i,
- 27*sizeof(t_list));
+ /* in first j loop, 3bp run can be skipped */
+ if(!(moldyn->run3bp))
+ continue;
+
+ /* first loop over atoms k */
+ if(moldyn->func3b_k1) {
- /* get neighbours of i */
for(k=0;k<27;k++) {
+ 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);
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_k1(moldyn,
+ &(itom[i]),
+ jtom,
+ ktom,
+ bc_ik|bc_ij);
+#ifdef STATIC_LISTS
+ }
+#else
+ } while(list_next_f(that)!=\
+ L_NO_NEXT_ELEMENT);
+#endif
+
+ }
+
+ }
+
+ if(moldyn->func3b_j2)
+ moldyn->func3b_j2(moldyn,
+ &(itom[i]),
+ jtom,
+ bc_ij);
+
+ /* second loop over atoms k */
+ if(moldyn->func3b_k2) {
+
+ for(k=0;k<27;k++) {
+
bc_ik=(k<dnlc)?0:1;
+#ifdef STATIC_LISTS
+ q=0;
- do {
+ 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)
+ continue;
+ do {
ktom=that->current->data;
+#endif
if(!(ktom->attr&ATOM_ATTR_3BP))
continue;
if(ktom==&(itom[i]))
continue;
- moldyn->func3b(moldyn,
- &(itom[i]),
- jtom,
- ktom,
- bc_ik|bc_ij);
+ 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->func2b_post) {
- moldyn->func2b_post(moldyn,
- &(itom[i]),
- jtom,bc_ij);
+ 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("\n\n");
-#endif
-#ifdef VDEBUG
-printf("\n\n");
+ //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[5832].f.x);
+ printf(" y: %0.40f\n",moldyn->atom[5832].f.y);
+ printf(" z: %0.40f\n",moldyn->atom[5832].f.z);
+ }
#endif
+ /* calculate global virial */
+ for(i=0;i<count;i++) {
+ moldyn->gvir.xx+=moldyn->atom[i].r.x*moldyn->atom[i].f.x;
+ moldyn->gvir.yy+=moldyn->atom[i].r.y*moldyn->atom[i].f.y;
+ moldyn->gvir.zz+=moldyn->atom[i].r.z*moldyn->atom[i].f.z;
+ moldyn->gvir.xy+=moldyn->atom[i].r.y*moldyn->atom[i].f.x;
+ moldyn->gvir.xz+=moldyn->atom[i].r.z*moldyn->atom[i].f.x;
+ moldyn->gvir.yz+=moldyn->atom[i].r.z*moldyn->atom[i].f.y;
+ }
+
return 0;
}
}
/*
- * periodic boundayr checking
+ * periodic boundary checking
*/
//inline int check_per_bound(t_moldyn *moldyn,t_3dvec *a) {
return 0;
}
+
+/*
+ * restore function
+ */
+
+int moldyn_read_save_file(t_moldyn *moldyn,char *file) {
+
+ int fd;
+ int cnt,size;
+
+ fd=open(file,O_RDONLY);
+ if(fd<0) {
+ perror("[moldyn] load save file open");
+ return fd;
+ }
+
+ size=sizeof(t_moldyn);
+
+ 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);
+
+ 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;
+}
+
+int moldyn_load(t_moldyn *moldyn) {
+
+ // later ...
+
+ 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;
+ }
+}
+
+int pair_correlation_init(t_moldyn *moldyn,double dr) {
+
+
+ return 0;
+}
+
+int calculate_pair_correlation(t_moldyn *moldyn,double dr,void *ptr) {
+
+ int slots;
+ double *stat;
+ int i,j;
+ t_linkcell *lc;
+#ifdef STATIC_LISTS
+ int *neighbour[27];
+ int p;
+#else
+ t_list neighbour[27];
+#endif
+ t_atom *itom,*jtom;
+ t_list *this;
+ unsigned char bc;
+ t_3dvec dist;
+ double d;
+ //double norm;
+ int o,s;
+ unsigned char ibrand;
+
+ lc=&(moldyn->lc);
+
+ slots=moldyn->cutoff/dr;
+ o=2*slots;
+
+ 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(ptr!=NULL) {
+ stat=(double *)ptr;
+ }
+ else {
+ stat=(double *)malloc(3*slots*sizeof(double));
+ if(stat==NULL) {
+ perror("[moldyn] pair correlation malloc");
+ return -1;
+ }
+ }
+
+ memset(stat,0,3*slots*sizeof(double));
+
+ 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);
+
+ /* brand of atom i */
+ ibrand=itom[i].brand;
+
+ 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
+ /* only count pairs once,
+ * skip same atoms */
+ if(itom[i].tag>=jtom->tag)
+ continue;
+
+ /*
+ * pair correlation calc
+ */
+
+ /* distance */
+ v3_sub(&dist,&(jtom->r),&(itom[i].r));
+ if(bc) check_per_bound(moldyn,&dist);
+ d=v3_absolute_square(&dist);
+
+ /* ignore if greater or equal cutoff */
+ if(d>=moldyn->cutoff_square)
+ continue;
+
+ /* fill the slots */
+ d=sqrt(d);
+ s=(int)(d/dr);
+
+ /* should never happen but it does 8) -
+ * related to -ffloat-store problem! */
+ if(s>=slots) s=slots-1;
+
+ if(ibrand!=jtom->brand) {
+ /* mixed */
+ stat[s]+=1;
+ }
+ else {
+ /* type a - type a bonds */
+ if(ibrand==0)
+ stat[s+slots]+=1;
+ else
+ /* type b - type b bonds */
+ stat[s+o]+=1;
+ }
+#ifdef STATIC_LISTS
+ }
+#else
+ } while(list_next_f(this)!=L_NO_NEXT_ELEMENT);
+#endif
+ }
+ }
+
+ /* normalization
+ for(i=1;i<slots;i++) {
+ // normalization: 4 pi r r dr
+ // here: not double counting pairs -> 2 pi r r dr
+ norm=2*M_PI*moldyn->count*(i*dr*i*dr)*dr;
+ stat[i]/=norm;
+ stat[slots+i]/=norm;
+ stat[o+i]/=norm;
+ }
+ */
+
+ if(ptr==NULL) {
+ /* todo: store/print pair correlation function */
+ free(stat);
+ }
+
+ free(moldyn->atom);
+
+ link_cell_shutdown(moldyn);
+
+ return 0;
+}
+
+int analyze_bonds(t_moldyn *moldyn) {
+
+
+
+
+ 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;
+ }
+
+ /* write the actual data file */
+
+ // 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);
+
+ // 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
+ }
+ }
+
+ // 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);
+
+ return 0;
+}
+
projects / physik / posic.git / blobdiff