#include <math.h>
#include "moldyn.h"
-
-#include "math/math.h"
-#include "init/init.h"
-#include "random/random.h"
-#include "visual/visual.h"
-#include "list/list.h"
-
+#include "report/report.h"
int moldyn_init(t_moldyn *moldyn,int argc,char **argv) {
- //int ret;
-
- //ret=moldyn_parse_argv(moldyn,argc,argv);
- //if(ret<0) return ret;
+ printf("[moldyn] init\n");
memset(moldyn,0,sizeof(t_moldyn));
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;
}
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;
}
+ moldyn->dv=0.000001*moldyn->volume;
+
+ 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");
+ printf(" delta volume (pressure calc): %f\n",moldyn->dv);
+
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_potential1b(t_moldyn *moldyn,pf_func1b func) {
moldyn->func1b=func;
- moldyn->pot1b_params=params;
return 0;
}
-int set_potential2b(t_moldyn *moldyn,pf_func2b func,void *params) {
+int set_potential2b(t_moldyn *moldyn,pf_func2b func) {
moldyn->func2b=func;
- moldyn->pot2b_params=params;
return 0;
}
-int set_potential3b(t_moldyn *moldyn,pf_func3b func,void *params) {
+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->func3b_k1=func;
+
+ return 0;
+}
+
+int set_potential3b_k2(t_moldyn *moldyn,pf_func3b func) {
+
+ moldyn->func3b_k2=func;
+
+ return 0;
+}
+
+int set_potential_params(t_moldyn *moldyn,void *params) {
+
+ moldyn->pot_params=params;
+
+ return 0;
+}
+
+int moldyn_set_log_dir(t_moldyn *moldyn,char *dir) {
+
+ strncpy(moldyn->vlsdir,dir,127);
+
+ return 0;
+}
+
+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 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);
+ ret=visual_init(&(moldyn->vis),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->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",moldyn->vlsdir);
+ system(sc);
+ snprintf(sc,255,"cd %s && pdflatex report",moldyn->vlsdir);
+ system(sc);
+ snprintf(sc,255,"cd %s && dvipdf report",moldyn->vlsdir);
+ system(sc);
+ }
if(&(moldyn->vis)) visual_tini(&(moldyn->vis));
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) {
- int count;
+ int new,count;
int ret;
t_3dvec origin;
+ void *ptr;
+ t_atom *atom;
- count=a*b*c;
-
- 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!) */
+ origin.x=0.5*lc;
+ origin.y=0.5*lc;
+ origin.z=0.5*lc;
switch(type) {
+ case CUBIC:
+ set_nn_dist(moldyn,lc);
+ ret=cubic_init(a,b,c,lc,atom,&origin);
+ break;
case FCC:
- ret=fcc_init(a,b,c,lc,moldyn->atom,&origin);
+ v3_scale(&origin,&origin,0.5);
+ set_nn_dist(moldyn,0.5*sqrt(2.0)*lc);
+ ret=fcc_init(a,b,c,lc,atom,&origin);
break;
case DIAMOND:
- ret=diamond_init(a,b,c,lc,moldyn->atom,&origin);
+ v3_scale(&origin,&origin,0.25);
+ set_nn_dist(moldyn,0.25*sqrt(3.0)*lc);
+ ret=diamond_init(a,b,c,lc,atom,&origin);
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);
+ moldyn->count+=new;
+ printf("[moldyn] created lattice with %d atoms\n",new);
- 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));
+ 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));
}
-
return ret;
}
-int add_atom(t_moldyn *moldyn,int element,double mass,u8 bnum,u8 attr,
+/* 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 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)++;
- 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;
+ 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;
}
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 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);
+ moldyn->t_sum+=moldyn->t;
+ moldyn->mean_t=moldyn->t_sum/moldyn->total_steps;
+
+ 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) {
+double ideal_gas_law_pressure(t_moldyn *moldyn) {
+
+ double p;
+
+ p=moldyn->count*moldyn->t*K_BOLTZMANN/moldyn->volume;
+
+ return p;
+}
+
+double pressure_calc(t_moldyn *moldyn) {
int i;
- t_atom *atom;
+ double v;
+ t_virial *virial;
- atom=moldyn->atom;
- moldyn->ekin=0.0;
+ /*
+ * PV = NkT + <W>
+ * W = 1/3 sum_i f_i r_i
+ * virial = sum_i f_i r_i
+ *
+ * => P = (2 Ekin + virial) / (3V)
+ */
- for(i=0;i<moldyn->count;i++)
- moldyn->ekin+=0.5*atom[i].mass*v3_absolute_square(&(atom[i].v));
+ v=0.0;
+ for(i=0;i<moldyn->count;i++) {
+ virial=&(moldyn->atom[i].virial);
+ v+=(virial->xx+virial->yy+virial->zz);
+ }
- return moldyn->ekin;
+ /* assume up to date kinetic energy */
+ moldyn->p=2.0*moldyn->ekin+v;
+ moldyn->p/=(3.0*moldyn->volume);
+ moldyn->p_sum+=moldyn->p;
+ moldyn->mean_p=moldyn->p_sum/moldyn->total_steps;
+
+ /* pressure from 'absolute coordinates' virial */
+ virial=&(moldyn->virial);
+ v=virial->xx+virial->yy+virial->zz;
+ moldyn->gp=2.0*moldyn->ekin+v;
+ moldyn->gp/=(3.0*moldyn->volume);
+ moldyn->gp_sum+=moldyn->gp;
+ moldyn->mean_gp=moldyn->gp_sum/moldyn->total_steps;
+
+ return moldyn->p;
+}
+
+double thermodynamic_pressure_calc(t_moldyn *moldyn) {
+
+ t_3dvec dim,*tp;
+ double u,p;
+ double scale,dv;
+ t_atom *store;
+
+ /*
+ * dU = - p dV
+ *
+ * => p = - dU/dV
+ *
+ * dV: dx,y,z = 0.001 x,y,z
+ */
+
+ scale=1.00000000000001;
+printf("\n\nP-DEBUG:\n");
+
+ tp=&(moldyn->tp);
+ store=malloc(moldyn->count*sizeof(t_atom));
+ if(store==NULL) {
+ printf("[moldyn] allocating store mem failed\n");
+ return -1;
+ }
+
+ /* 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_dim(moldyn,scale,TRUE,0,0);
+ scale_atoms(moldyn,scale,TRUE,0,0);
+ dv=0.00000000000001*moldyn->dim.x*moldyn->dim.y*moldyn->dim.z;
+ link_cell_shutdown(moldyn);
+ link_cell_init(moldyn,QUIET);
+ potential_force_calc(moldyn);
+ tp->x=(moldyn->energy-u)/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_dim(moldyn,scale,0,TRUE,0);
+ scale_atoms(moldyn,scale,0,TRUE,0);
+ dv=0.00000000000001*moldyn->dim.y*moldyn->dim.x*moldyn->dim.z;
+ link_cell_shutdown(moldyn);
+ link_cell_init(moldyn,QUIET);
+ potential_force_calc(moldyn);
+ tp->y=(moldyn->energy-u)/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_dim(moldyn,scale,0,0,TRUE);
+ scale_atoms(moldyn,scale,0,0,TRUE);
+ dv=0.00000000000001*moldyn->dim.z*moldyn->dim.x*moldyn->dim.y;
+ link_cell_shutdown(moldyn);
+ link_cell_init(moldyn,QUIET);
+ potential_force_calc(moldyn);
+ tp->z=(moldyn->energy-u)/dv;
+ p+=tp->z*tp->z;
+
+ /* restore atomic configuration + dim */
+ memcpy(moldyn->atom,store,moldyn->count*sizeof(t_atom));
+ moldyn->dim=dim;
+
+ /* restore energy */
+ moldyn->energy=u;
+
+ link_cell_shutdown(moldyn);
+ link_cell_init(moldyn,QUIET);
+
+ return sqrt(p);
}
-double get_e_pot(t_moldyn *moldyn) {
+double get_pressure(t_moldyn *moldyn) {
+
+ return moldyn->p;
- return moldyn->energy;
}
-double update_e_kin(t_moldyn *moldyn) {
+int scale_dim(t_moldyn *moldyn,double scale,u8 x,u8 y,u8 z) {
+
+ t_3dvec *dim;
- return(get_e_kin(moldyn));
+ dim=&(moldyn->dim);
+
+ 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 i;
+ t_3dvec *r;
+
+ 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);
+ }
+moldyn->debug=scale;
+
+ /* scale the atoms and dimensions */
+ scale_atoms(moldyn,scale,TRUE,TRUE,TRUE);
+ scale_dim(moldyn,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++)
+ moldyn->ekin+=0.5*atom[i].mass*v3_absolute_square(&(atom[i].v));
+
+ return moldyn->ekin;
}
double get_total_energy(t_moldyn *moldyn) {
/* nn_dist is the nearest neighbour distance */
- if(moldyn->t==5.0) {
- printf("[moldyn] i do not estimate timesteps below %f K!\n",
- MOLDYN_CRITICAL_EST_TEMP);
- return 23.42;
- }
-
tau=(0.05*nn_dist*moldyn->atom[0].mass)/sqrt(3.0*K_BOLTZMANN*moldyn->t);
return tau;
/* linked list / cell method */
-int link_cell_init(t_moldyn *moldyn) {
+int link_cell_init(t_moldyn *moldyn,u8 vol) {
t_linkcell *lc;
int i;
- int fd;
-
- fd=open("/dev/null",O_WRONLY);
lc=&(moldyn->lc);
lc->cells=lc->nx*lc->ny*lc->nz;
lc->subcell=malloc(lc->cells*sizeof(t_list));
- printf("[moldyn] initializing linked cells (%d)\n",lc->cells);
+ if(lc->cells<27)
+ printf("[moldyn] FATAL: less then 27 subcells!\n");
+
+ if(vol) {
+ printf("[moldyn] initializing linked cells (%d)\n",lc->cells);
+ 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);
+ }
for(i=0;i<lc->cells;i++)
- //list_init(&(lc->subcell[i]),1);
- list_init(&(lc->subcell[i]),fd);
+ list_init_f(&(lc->subcell[i]));
link_cell_update(moldyn);
int link_cell_update(t_moldyn *moldyn) {
int count,i,j,k;
- int nx,ny,nz;
+ int nx,ny;
t_atom *atom;
t_linkcell *lc;
+ double x,y,z;
atom=moldyn->atom;
lc=&(moldyn->lc);
nx=lc->nx;
ny=lc->ny;
- nz=lc->nz;
+
+ x=moldyn->dim.x/2;
+ y=moldyn->dim.y/2;
+ z=moldyn->dim.z/2;
for(i=0;i<lc->cells;i++)
- list_destroy(&(moldyn->lc.subcell[i]));
+ list_destroy_f(&(lc->subcell[i]));
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]));
+ 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(&(lc->subcell[i+j*nx+k*nx*ny]),
+ &(atom[count]));
}
return 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]));
+ list_destroy_f(&(moldyn->lc.subcell[i]));
+
+ 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;
+ t_3dvec momentum;
+ t_moldyn_schedule *sched;
t_atom *atom;
int fd;
- char fb[128];
+ char dir[128];
double ds;
+ double energy_scale;
+ //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;
+ 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;
+
/* calculate initial forces */
potential_force_calc(moldyn);
- /* 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");
if(moldyn->cutoff>0.5*moldyn->dim.y)
/* 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 */
+ for(sched->count=0;sched->count<sched->total_sched;sched->count++) {
/* 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];
/* integration according to schedule */
/* integration step */
moldyn->integrate(moldyn);
+ /* calculate kinetic energy, temperature and pressure */
+ e_kin_calc(moldyn);
+ temperature_calc(moldyn);
+ pressure_calc(moldyn);
+ //tp=thermodynamic_pressure_calc(moldyn);
+//printf("thermodynamic p: %f %f %f - %f\n",moldyn->tp.x/BAR,moldyn->tp.y/BAR,moldyn->tp.z/BAR,tp/BAR);
+
/* 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))
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);
+ 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(!(i%p)) {
+ dprintf(moldyn->pfd,
+ "%f %f %f %f %f\n",moldyn->time,
+ moldyn->p/BAR,moldyn->mean_p/BAR,
+ moldyn->gp/BAR,moldyn->mean_gp/BAR);
+ }
+ }
+ if(t) {
+ if(!(i%t)) {
+ dprintf(moldyn->tfd,
+ "%f %f %f\n",
+ moldyn->time,moldyn->t,moldyn->mean_t);
}
}
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);
+ snprintf(dir,128,"%s/s-%07.f.save",
+ moldyn->vlsdir,moldyn->time);
+ fd=open(dir,O_WRONLY|O_TRUNC|O_CREAT);
if(fd<0) perror("[moldyn] save fd open");
else {
write(fd,moldyn,sizeof(t_moldyn));
if(!(i%v)) {
visual_atoms(&(moldyn->vis),moldyn->time,
moldyn->atom,moldyn->count);
- printf("\rsched: %d, steps: %d",sched,i);
- fflush(stdout);
}
}
+ /* display progress */
+ if(!(i%10)) {
+ printf("\rsched: %d, steps: %d, T: %f, P: %f %f V: %f",
+ sched->count,i,
+ moldyn->mean_t,
+ moldyn->mean_p/BAR,
+ moldyn->mean_gp/BAR,
+ moldyn->volume);
+ fflush(stdout);
+ }
+
+ /* 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)
+ sched->hook(moldyn,sched->hook_params);
+
+ /* get a new info line */
+ printf("\n");
}
int velocity_verlet(t_moldyn *moldyn) {
int i,count;
- double tau,tau_square;
+ double tau,tau_square,h;
t_3dvec delta;
t_atom *atom;
for(i=0;i<count;i++) {
/* 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);
}
/* forces depending on chosen potential */
potential_force_calc(moldyn);
- //moldyn->potential_force_function(moldyn);
for(i=0;i<count;i++) {
- /* again velocities */
+ /* 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;
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;
+ u8 bc_ij,bc_ik;
+ int dnlc;
count=moldyn->count;
itom=moldyn->atom;
/* reset energy */
moldyn->energy=0.0;
+ /* reset global virial */
+ memset(&(moldyn->virial),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(!(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);
- countn=lc->countn;
- dnlc=lc->dnlc;
+ dnlc=lc->dnlc;
- for(j=0;j<countn;j++) {
+ /* first loop over atoms j */
+ if(moldyn->func2b) {
+ for(j=0;j<27;j++) {
this=&(neighbour_i[j]);
- list_reset(this);
+ list_reset_f(this);
if(this->start==NULL)
continue;
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);
-
- /* 3 body potential/force */
-
- if(!(itom[i].attr&ATOM_ATTR_3BP)||
- !(jtom->attr&ATOM_ATTR_3BP))
- continue;
-
- /*
- * according to mr. nordlund, we dont need to take the
- * sum over all atoms now, as 'this is centered' around
- * atom i ...
- * i am not quite sure though! there is a not vanishing
- * part even if f_c_ik is zero ...
- * this analytical potentials suck!
- * switching from mc to md to dft soon!
- */
-
- // 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);
-//
-// }
-
- /* copy the neighbour lists */
- memcpy(neighbour_i2,neighbour_i,
- 27*sizeof(t_list));
-
- /* get neighbours of i */
- for(k=0;k<countn;k++) {
+ bc_ij);
+ }
+ } while(list_next_f(this)!=L_NO_NEXT_ELEMENT);
- that=&(neighbour_i2[k]);
- list_reset(that);
-
- if(that->start==NULL)
- continue;
+ }
+ }
- bc_ijk=(k<dnlc)?0:1;
+ /* 3 body potential/force */
- do {
+ if(!(itom[i].attr&ATOM_ATTR_3BP))
+ continue;
- ktom=that->current->data;
+ /* copy the neighbour lists */
+ memcpy(neighbour_i2,neighbour_i,27*sizeof(t_list));
- if(!(ktom->attr&ATOM_ATTR_3BP))
- continue;
+ /* second loop over atoms j */
+ for(j=0;j<27;j++) {
- if(ktom==jtom)
- continue;
+ this=&(neighbour_i[j]);
+ list_reset_f(this);
- if(ktom==&(itom[i]))
+ if(this->start==NULL)
continue;
-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);
-
- } while(list_next(that)!=\
- L_NO_NEXT_ELEMENT);
-
- }
-
- } while(list_next(this)!=L_NO_NEXT_ELEMENT);
- }
- }
- }
+ bc_ij=(j<dnlc)?0:1;
- return 0;
-}
+ do {
+ jtom=this->current->data;
-/*
- * periodic boundayr checking
- */
+ if(jtom==&(itom[i]))
+ continue;
-int check_per_bound(t_moldyn *moldyn,t_3dvec *a) {
-
- double x,y,z;
- t_3dvec *dim;
+ if(!(jtom->attr&ATOM_ATTR_3BP))
+ continue;
- dim=&(moldyn->dim);
+ /* reset 3bp run */
+ moldyn->run3bp=1;
- x=0.5*dim->x;
- y=0.5*dim->y;
- z=0.5*dim->z;
+ if(moldyn->func3b_j1)
+ moldyn->func3b_j1(moldyn,
+ &(itom[i]),
+ jtom,
+ bc_ij);
- if(moldyn->status&MOLDYN_STAT_PBX) {
- if(a->x>=x) a->x-=dim->x;
- else if(-a->x>x) a->x+=dim->x;
- }
- if(moldyn->status&MOLDYN_STAT_PBY) {
- if(a->y>=y) a->y-=dim->y;
- else if(-a->y>y) a->y+=dim->y;
- }
- if(moldyn->status&MOLDYN_STAT_PBZ) {
- if(a->z>=z) a->z-=dim->z;
- else if(-a->z>z) a->z+=dim->z;
- }
+ /* in first j loop, 3bp run can be skipped */
+ if(!(moldyn->run3bp))
+ continue;
+
+ /* first loop over atoms k */
+ if(moldyn->func3b_k1) {
- return 0;
-}
-
+ for(k=0;k<27;k++) {
-/*
- * example potentials
- */
+ that=&(neighbour_i2[k]);
+ list_reset_f(that);
+
+ if(that->start==NULL)
+ continue;
-/* harmonic oscillator potential and force */
+ bc_ik=(k<dnlc)?0:1;
-int harmonic_oscillator(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
+ do {
- t_ho_params *params;
- t_3dvec force,distance;
- double d;
- double sc,equi_dist;
+ ktom=that->current->data;
- params=moldyn->pot2b_params;
- sc=params->spring_constant;
- equi_dist=params->equilibrium_distance;
+ if(!(ktom->attr&ATOM_ATTR_3BP))
+ continue;
- 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);
- }
+ if(ktom==jtom)
+ continue;
- return 0;
-}
+ if(ktom==&(itom[i]))
+ continue;
-/* 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);
- }
+ moldyn->func3b_k1(moldyn,
+ &(itom[i]),
+ jtom,
+ ktom,
+ bc_ik|bc_ij);
- return 0;
-}
+ } while(list_next_f(that)!=\
+ L_NO_NEXT_ELEMENT);
-/*
- * tersoff potential & force for 2 sorts of atoms
- */
+ }
-/* 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]);
+ if(moldyn->func3b_j2)
+ moldyn->func3b_j2(moldyn,
+ &(itom[i]),
+ jtom,
+ bc_ij);
- return 0;
-}
+ /* second loop over atoms k */
+ if(moldyn->func3b_k2) {
-/* tersoff 1 body part */
-int tersoff_mult_1bp(t_moldyn *moldyn,t_atom *ai) {
+ for(k=0;k<27;k++) {
- int num;
- t_tersoff_mult_params *params;
- t_tersoff_exchange *exchange;
-
- num=ai->bnum;
- params=moldyn->pot1b_params;
- exchange=&(params->exchange);
+ that=&(neighbour_i2[k]);
+ list_reset_f(that);
+
+ if(that->start==NULL)
+ continue;
- /*
- * simple: point constant parameters only depending on atom i to
- * their right values
- */
+ bc_ik=(k<dnlc)?0:1;
- 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]);
+ do {
- exchange->betan=pow(*(exchange->beta),*(exchange->n));
- exchange->c2=params->c[num]*params->c[num];
- exchange->d2=params->d[num]*params->d[num];
- exchange->c2d2=exchange->c2/exchange->d2;
+ ktom=that->current->data;
- 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;
+ if(!(ktom->attr&ATOM_ATTR_3BP))
+ continue;
- params=moldyn->pot2b_params;
- num=ai->bnum;
- exchange=&(params->exchange);
+ if(ktom==jtom)
+ continue;
- exchange->run3bp=0;
-
- /*
- * we need: f_c, df_c, f_r, df_r
- *
- * therefore we need: R, S, A, lambda
- */
+ if(ktom==&(itom[i]))
+ continue;
- v3_sub(&dist_ij,&(ai->r),&(aj->r));
+ moldyn->func3b_k2(moldyn,
+ &(itom[i]),
+ jtom,
+ ktom,
+ bc_ik|bc_ij);
- if(bc) check_per_bound(moldyn,&dist_ij);
+ } while(list_next_f(that)!=\
+ L_NO_NEXT_ELEMENT);
- d_ij=v3_norm(&dist_ij);
+ }
+
+ }
- /* save for use in 3bp */
- exchange->d_ij=d_ij;
- exchange->dist_ij=dist_ij;
- exchange->d_ij2=d_ij*d_ij;
+ /* 2bp post function */
+ if(moldyn->func3b_j3) {
+ moldyn->func3b_j3(moldyn,
+ &(itom[i]),
+ jtom,bc_ij);
+ }
+
+ } while(list_next_f(this)!=L_NO_NEXT_ELEMENT);
+
+ }
+
+#ifdef DEBUG
+ //printf("\n\n");
+#endif
+#ifdef VDEBUG
+ printf("\n\n");
+#endif
- /* 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;
- }
- 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;
}
- if(d_ij>S)
- return 0;
+#ifdef DEBUG
+ printf("\nATOM 0: %f %f %f\n\n",itom->f.x,itom->f.y,itom->f.z);
+#endif
- f_r=A*exp(-lambda*d_ij);
- df_r=-lambda*f_r/d_ij;
-
- /* f_a, df_a calc + save for 3bp use */
- exchange->f_a=-B*exp(-mu*d_ij);
- exchange->df_a=-mu*exchange->f_a/d_ij;
-
- 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);
- }
- 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);
+ /* calculate global virial */
+ for(i=0;i<count;i++) {
+ moldyn->virial.xx+=moldyn->atom[i].r.x*moldyn->atom[i].f.x;
+ moldyn->virial.yy+=moldyn->atom[i].r.y*moldyn->atom[i].f.y;
+ moldyn->virial.zz+=moldyn->atom[i].r.z*moldyn->atom[i].f.z;
+ moldyn->virial.xy+=moldyn->atom[i].r.y*moldyn->atom[i].f.x;
+ moldyn->virial.xz+=moldyn->atom[i].r.z*moldyn->atom[i].f.x;
+ moldyn->virial.yz+=moldyn->atom[i].r.z*moldyn->atom[i].f.y;
}
- /* 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);
-
- /* save for use in 3bp */
- exchange->f_c=f_c;
- exchange->df_c=df_c;
-
- /* enable the run of 3bp function */
- exchange->run3bp=1;
-
return 0;
}
-/* tersoff 3 body part */
+/*
+ * virial calculation
+ */
-int tersoff_mult_3bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,t_atom *ak,u8 bc) {
+//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) {
- 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,b_ij,f_a,df_a;
- double f_c_ik,df_c_ik,arg;
- double scale;
- double chi;
- double n,c,d,h,beta,betan;
- double c2,d2,c2d2;
- double numer,denom;
- double theta,cos_theta,sin_theta;
- double d_theta,d_theta1,d_theta2;
- double h_cos,h_cos2,d2_h_cos2;
- double frac1,bracket1,bracket2,bracket2_n_1,bracket2_n;
- double bracket3,bracket3_pow_1,bracket3_pow;
- int num;
-
- params=moldyn->pot3b_params;
- num=ai->bnum;
- exchange=&(params->exchange);
-
- if(!(exchange->run3bp))
- return 0;
+ 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;
- /*
- * 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
- */
+ return 0;
+}
- d_ij=exchange->d_ij;
- d_ij2=exchange->d_ij2;
+/*
+ * periodic boundayr checking
+ */
- f_a=params->exchange.f_a;
- df_a=params->exchange.df_a;
+//inline int check_per_bound(t_moldyn *moldyn,t_3dvec *a) {
+int check_per_bound(t_moldyn *moldyn,t_3dvec *a) {
- /* d_ij is <= S, as we didn't return so far! */
-
- /*
- * 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,
- *
- */
+ double x,y,z;
+ t_3dvec *dim;
- v3_sub(&dist_ik,&(ai->r),&(ak->r));
- if(bc) check_per_bound(moldyn,&dist_ik);
- d_ik=v3_norm(&dist_ik);
+ dim=&(moldyn->dim);
- /* 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;
- }
+ x=dim->x/2;
+ y=dim->y/2;
+ z=dim->z/2;
- /* calc of f_c_ik */
- if(d_ik>S) {
- f_c_ik=0.0;
- df_c_ik=0.0;
- }
- else if(d_ik<R) {
- f_c_ik=1.0;
- df_c_ik=0.0;
- }
- 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));
+ if(moldyn->status&MOLDYN_STAT_PBX) {
+ if(a->x>=x) a->x-=dim->x;
+ else if(-a->x>x) a->x+=dim->x;
}
-
- v3_sub(&dist_jk,&(aj->r),&(ak->r));
- if(bc) check_per_bound(moldyn,&dist_jk);
- d_jk=v3_norm(&dist_jk);
-
- beta=*(exchange->beta);
- betan=exchange->betan;
- n=*(exchange->n);
- c=*(exchange->c);
- d=*(exchange->d);
- h=*(exchange->h);
- chi=exchange->chi;
- 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;
- 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);
- h_cos2=h_cos*h_cos;
- d2_h_cos2=d2-h_cos2;
-
- /* some usefull expressions */
- frac1=c2/(d2-h_cos2);
- bracket1=1+c2d2-frac1;
- if(f_c_ik==0.0) {
- bracket2=0.0;
- bracket2_n_1=0.0;
- bracket2_n=0.0;
- bracket3=1.0;
- printf("Foo -> 0: ");
+ if(moldyn->status&MOLDYN_STAT_PBY) {
+ if(a->y>=y) a->y-=dim->y;
+ else if(-a->y>y) a->y+=dim->y;
}
- else {
- bracket2=f_c_ik*bracket1;
- bracket2_n_1=pow(bracket2,n-1.0);
- bracket2_n=bracket2_n_1*bracket2;
- bracket3=1.0+betan*bracket2_n;
- printf("Foo -> 1: ");
+ if(moldyn->status&MOLDYN_STAT_PBZ) {
+ if(a->z>=z) a->z-=dim->z;
+ else if(-a->z>z) a->z+=dim->z;
}
- bracket3_pow_1=pow(bracket3,(-1.0/(2.0*n))-1.0);
-printf("THETA: %.15f %.15f\n",cos_theta,theta*180/(2*M_PI));
- bracket3_pow=bracket3_pow_1*bracket3;
-
- /* now go on with calc of b_ij and derivation of b_ij */
- b_ij=chi*bracket3_pow;
-
- /* derivation of theta */
- v3_scale(&force,&dist_ij,d_theta1);
- v3_scale(&temp,&dist_ik,d_theta2);
- v3_add(&force,&force,&temp);
-
- /* part 1 of derivation of b_ij */
- v3_scale(&force,&force,sin_theta*2*h_cos*f_c_ik*frac1);
-
- /* part 2 of derivation of b_ij */
- v3_scale(&temp,&dist_ik,df_c_ik*bracket1);
-
- /* sum up and scale ... */
- v3_add(&temp,&temp,&force);
- scale=bracket2_n_1*n*betan*(1+betan*bracket3_pow_1)*chi*(1.0/(2.0*n));
- v3_scale(&temp,&temp,scale);
-
- /* now construct an energy and a force out of that */
- v3_scale(&temp,&temp,f_a);
- v3_scale(&force,&dist_ij,df_a*b_ij);
- v3_add(&temp,&temp,&force);
- v3_scale(&temp,&temp,f_c);
- v3_scale(&force,&dist_ij,df_c*b_ij*f_a);
- v3_add(&force,&force,&temp);
-
- /* add forces */
- v3_add(&(ai->f),&(ai->f),&force);
- /* energy is 0.5 f_r f_c */
- moldyn->energy+=(0.5*f_a*b_ij*f_c);
-
+
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;
+}