#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: %f\n",moldyn->t_ref);
+
+ return 0;
+}
+
+int set_pressure(t_moldyn *moldyn,double p_ref) {
+
+ moldyn->p_ref=p_ref;
+
+ printf("[moldyn] pressure: %f\n",moldyn->p_ref);
+
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;
}
return 0;
}
-int moldyn_set_log(t_moldyn *moldyn,u8 type,char *fb,int timer) {
+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) {
+
+ 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;
+
+ 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 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;
+ }
+ 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;
+ }
+ dprintf(moldyn->rfd,report_start,
+ moldyn->rauthor,moldyn->rtitle);
+ dprintf(moldyn->pfd,plot_script);
+ close(moldyn->pfd);
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->mfd) close(moldyn->mfd);
+ 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);
+ 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);
switch(type) {
+ case CUBIC:
+ origin.x=0.5*lc;
+ origin.y=0.5*lc;
+ origin.z=0.5*lc;
+ ret=cubic_init(a,b,c,lc,atom,&origin);
+ break;
case FCC:
- ret=fcc_init(a,b,c,lc,moldyn->atom,&origin);
+ ret=fcc_init(a,b,c,lc,atom,NULL);
break;
case DIAMOND:
- ret=diamond_init(a,b,c,lc,moldyn->atom,&origin);
+ 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;
+ t_3dvec o,r,n;
+ t_3dvec basis[3];
+ double help[3];
+ double x,y,z;
+
+ x=a*lc;
+ y=b*lc;
+ z=c*lc;
+
+ if(origin) v3_copy(&o,origin);
+ else v3_zero(&o);
+
+ /* construct the basis */
+ for(i=0;i<3;i++) {
+ for(j=0;j<3;j++) {
+ if(i!=j) help[j]=0.5*lc;
+ else help[j]=.0;
+ }
+ v3_set(&basis[i],help);
+ }
+
+ v3_zero(&r);
+ count=0;
+
+ /* fill up the room */
+ r.x=o.x;
+ while(r.x<x) {
+ r.y=o.y;
+ while(r.y<y) {
+ r.z=o.z;
+ while(r.z<z) {
+ v3_copy(&(atom[count].r),&r);
+ atom[count].element=1;
+ count+=1;
+ for(i=0;i<3;i++) {
+ v3_add(&n,&r,&basis[i]);
+ if((n.x<x+o.x)&&
+ (n.y<y+o.y)&&
+ (n.z<z+o.z)) {
+ v3_copy(&(atom[count].r),&n);
+ count+=1;
+ }
+ }
+ r.z+=lc;
+ }
+ r.y+=lc;
+ }
+ r.x+=lc;
+ }
+
+ /* coordinate transformation */
+ help[0]=x/2.0;
+ help[1]=y/2.0;
+ help[2]=z/2.0;
+ v3_set(&n,help);
+ for(i=0;i<count;i++)
+ v3_sub(&(atom[i].r),&(atom[i].r),&n);
+
+ 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);
+
+ 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 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;
+ double v;
+ t_virial *virial;
+
+ /*
+ * P = 1/(3V) sum_i ( p_i^2 / 2m + f_i r_i )
+ *
+ * virial = f_i r_i
+ */
+
+ v=0.0;
+ for(i=0;i<moldyn->count;i++) {
+ virial=&(moldyn->atom[i].virial);
+ v+=(virial->xx+virial->yy+virial->zz);
+ }
+
+ /* assume up to date kinetic energy */
+ moldyn->p=2.0*moldyn->ekin+v;
+ moldyn->p/=(3.0*moldyn->volume);
+
+ return moldyn->p;
+}
+
+double thermodynamic_pressure_calc(t_moldyn *moldyn) {
+
+ t_3dvec dim,*tp;
+ double u,p;
+ double scale;
+ t_atom *store;
+
+ 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=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);
+ 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);
+ 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);
+ link_cell_shutdown(moldyn);
+ link_cell_init(moldyn);
+ potential_force_calc(moldyn);
+ tp->z=(moldyn->energy-u)/moldyn->dv;
+ p+=tp->z*tp->z;
+
+ /* 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);
+ link_cell_shutdown(moldyn);
+ link_cell_init(moldyn);
+ 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);
+
+ /* 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);
+
+ return sqrt(p);
+}
+
+double get_pressure(t_moldyn *moldyn) {
+
+ return moldyn->p;
+
+}
+
+int scale_dim(t_moldyn *moldyn,double scale,u8 x,u8 y,u8 z) {
+
+ t_3dvec *dim;
+
+ 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_atom *atom;
+ t_3dvec *dim,*vdim;
+ double scale,v;
+ t_virial virial;
+ t_linkcell *lc;
+ int i;
+
+ atom=moldyn->atom;
+ dim=&(moldyn->dim);
+ vdim=&(moldyn->vis.dim);
+ lc=&(moldyn->lc);
+
+ memset(&virial,0,sizeof(t_virial));
+
+ for(i=0;i<moldyn->count;i++) {
+ virial.xx+=atom[i].virial.xx;
+ virial.yy+=atom[i].virial.yy;
+ virial.zz+=atom[i].virial.zz;
+ virial.xy+=atom[i].virial.xy;
+ virial.xz+=atom[i].virial.xz;
+ virial.yz+=atom[i].virial.yz;
+ }
+
+ /* just a guess so far ... */
+ v=virial.xx+virial.yy+virial.zz;
+
+printf("%f\n",v);
+ /* get pressure from virial */
+ moldyn->p=moldyn->count*K_BOLTZMANN*moldyn->t+ONE_THIRD*v;
+ moldyn->p/=moldyn->volume;
+printf("%f | %f\n",moldyn->p/(ATM),moldyn->p_ref/ATM);
+
+ /* scale factor */
+ if(moldyn->pt_scale&P_SCALE_BERENDSEN)
+ scale=3*sqrt(1-(moldyn->p_ref-moldyn->p)/moldyn->p_tc);
+ else
+ /* should actually never be used */
+ scale=pow(moldyn->p/moldyn->p_ref,1.0/3.0);
+
+printf("scale = %f\n",scale);
+ /* actual scaling */
+ dim->x*=scale;
+ dim->y*=scale;
+ dim->z*=scale;
+ if(vdim->x) vdim->x=dim->x;
+ if(vdim->y) vdim->y=dim->y;
+ if(vdim->z) vdim->z=dim->z;
+ moldyn->volume*=(scale*scale*scale);
+
+ /* check whether we need a new linkcell init */
+ if((dim->x/moldyn->cutoff!=lc->nx)||
+ (dim->y/moldyn->cutoff!=lc->ny)||
+ (dim->z/moldyn->cutoff!=lc->nx)) {
+ link_cell_shutdown(moldyn);
+ link_cell_init(moldyn);
+ }
return 0;
+
}
double get_e_kin(t_moldyn *moldyn) {
return moldyn->ekin;
}
-double get_e_pot(t_moldyn *moldyn) {
-
- return moldyn->energy;
-}
-
double update_e_kin(t_moldyn *moldyn) {
return(get_e_kin(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;
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));
+ if(lc->cells<27)
+ printf("[moldyn] FATAL: less then 27 subcells!\n");
+
printf("[moldyn] initializing linked cells (%d)\n",lc->cells);
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(&(moldyn->lc.subcell[i+j*nx+k*nx*ny]),
+ &(atom[count]));
}
return 0;
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;
+ int i;
unsigned int e,m,s,v;
t_3dvec p;
- t_moldyn_schedule *schedule;
+ t_moldyn_schedule *sched;
t_atom *atom;
int fd;
- char fb[128];
+ char dir[128];
double ds;
+ double energy_scale;
- schedule=&(moldyn->schedule);
+ sched=&(moldyn->schedule);
atom=moldyn->atom;
/* initialize linked cell method */
moldyn->tau_square=moldyn->tau*moldyn->tau;
moldyn->cutoff_square=moldyn->cutoff*moldyn->cutoff;
+ /* energy scaling factor */
+ energy_scale=moldyn->count*EV;
+
+printf("debug: %f\n",moldyn->atom[0].f.x);
/* calculate initial forces */
potential_force_calc(moldyn);
+printf("debug: %f\n",moldyn->atom[0].f.x);
/* some stupid checks before we actually start calculating bullshit */
if(moldyn->cutoff>0.5*moldyn->dim.x)
/* debugging, ignore */
moldyn->debug=0;
+ /* tell the world */
+ printf("[moldyn] integration start, go get a coffee ...\n");
+
/* executing the schedule */
- for(sched=0;sched<moldyn->schedule.content_count;sched++) {
+ 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 */
/* p/t scaling */
if(moldyn->pt_scale&(T_SCALE_BERENDSEN|T_SCALE_DIRECT))
scale_velocity(moldyn,FALSE);
+ if(moldyn->pt_scale&(P_SCALE_BERENDSEN|P_SCALE_DIRECT))
+ scale_volume(moldyn);
- /* increase absolute time */
- moldyn->time+=moldyn->tau;
+ update_e_kin(moldyn);
+ temperature_calc(moldyn);
+ pressure_calc(moldyn);
+ //thermodynamic_pressure_calc(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);
dprintf(moldyn->mfd,
- "%.15f %.45f\n",moldyn->time,
- v3_norm(&p));
+ "%f %f\n",moldyn->time,v3_norm(&p));
}
}
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, debug: %d",
- sched,i,moldyn->debug);
+ printf("\rsched: %d, steps: %d, debug: %f",
+ sched->count,i,moldyn->p/ATM);
fflush(stdout);
}
}
+ /* increase absolute time */
+ moldyn->time+=moldyn->tau;
+
}
/* 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);
}
potential_force_calc(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_ik;
int dnlc;
/* reset energy */
moldyn->energy=0.0;
- /* get energy and force of every atom */
+ /* 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 */
+ 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);
- dnlc=lc->dnlc;
+ dnlc=lc->dnlc;
- for(j=0;j<27;j++) {
+ for(j=0;j<27;j++) {
- this=&(neighbour_i[j]);
- list_reset(this);
+ this=&(neighbour_i[j]);
+ list_reset_f(this);
- if(this->start==NULL)
- continue;
+ if(this->start==NULL)
+ continue;
- bc_ij=(j<dnlc)?0:1;
+ bc_ij=(j<dnlc)?0:1;
- do {
- jtom=this->current->data;
+ do {
+ jtom=this->current->data;
- if(jtom==&(itom[i]))
- continue;
+ 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_2BP)&
+ (itom[i].attr&ATOM_ATTR_2BP)) {
+ moldyn->func2b(moldyn,
+ &(itom[i]),
+ jtom,
+ bc_ij);
+ }
- /* 3 body potential/force */
+ /* 3 body potential/force */
- if(!(itom[i].attr&ATOM_ATTR_3BP)||
- !(jtom->attr&ATOM_ATTR_3BP))
- continue;
+ if(!(itom[i].attr&ATOM_ATTR_3BP)||
+ !(jtom->attr&ATOM_ATTR_3BP))
+ continue;
- /* copy the neighbour lists */
- memcpy(neighbour_i2,neighbour_i,
- 27*sizeof(t_list));
+ /* copy the neighbour lists */
+ memcpy(neighbour_i2,neighbour_i,
+ 27*sizeof(t_list));
- /* get neighbours of i */
- for(k=0;k<27;k++) {
+ /* get neighbours of i */
+ for(k=0;k<27;k++) {
- that=&(neighbour_i2[k]);
- list_reset(that);
+ that=&(neighbour_i2[k]);
+ list_reset_f(that);
- if(that->start==NULL)
- continue;
+ if(that->start==NULL)
+ continue;
- bc_ik=(k<dnlc)?0:1;
+ bc_ik=(k<dnlc)?0:1;
- do {
+ do {
- ktom=that->current->data;
+ ktom=that->current->data;
- if(!(ktom->attr&ATOM_ATTR_3BP))
- continue;
+ if(!(ktom->attr&ATOM_ATTR_3BP))
+ continue;
- if(ktom==jtom)
- continue;
+ if(ktom==jtom)
+ continue;
- if(ktom==&(itom[i]))
- continue;
+ if(ktom==&(itom[i]))
+ continue;
+
+ moldyn->func3b(moldyn,
+ &(itom[i]),
+ jtom,
+ ktom,
+ bc_ik|bc_ij);
- moldyn->func3b(moldyn,&(itom[i]),jtom,ktom,bc_ik|bc_ij);
+ } while(list_next_f(that)!=\
+ L_NO_NEXT_ELEMENT);
- } while(list_next(that)!=\
- L_NO_NEXT_ELEMENT);
+ }
- }
-
- } while(list_next(this)!=L_NO_NEXT_ELEMENT);
-
/* 2bp post function */
if(moldyn->func2b_post) {
moldyn->func2b_post(moldyn,
&(itom[i]),
jtom,bc_ij);
}
-
- }
+
+ } while(list_next_f(this)!=L_NO_NEXT_ELEMENT);
+
}
-//printf("DEBUG: %.15f \n",itom[i].f.x);
+
}
+#ifdef DEBUG
+printf("\n\n");
+#endif
+#ifdef VDEBUG
+printf("\n\n");
+#endif
+
+ return 0;
+}
+
+/*
+ * virial calculation
+ */
+
+inline 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 boundayr checking
*/
-int check_per_bound(t_moldyn *moldyn,t_3dvec *a) {
+inline int check_per_bound(t_moldyn *moldyn,t_3dvec *a) {
double x,y,z;
t_3dvec *dim;
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;
t_ho_params *params;
t_3dvec force,distance;
- double d;
+ double d,f;
double sc,equi_dist;
params=moldyn->pot2b_params;
sc=params->spring_constant;
equi_dist=params->equilibrium_distance;
+ if(ai<aj) return 0;
+
v3_sub(&distance,&(aj->r),&(ai->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));
+ moldyn->energy+=(0.5*sc*(d-equi_dist)*(d-equi_dist));
/* f = -grad E; grad r_ij = -1 1/r_ij distance */
- v3_scale(&force,&distance,sc*(1.0-(equi_dist/d)));
+ f=sc*(1.0-equi_dist/d);
+ v3_scale(&force,&distance,f);
v3_add(&(ai->f),&(ai->f),&force);
+ virial_calc(ai,&force,&distance);
+ virial_calc(aj,&force,&distance); /* f and d signe switched */
+ v3_scale(&force,&distance,-f);
+ v3_add(&(aj->f),&(aj->f),&force);
}
return 0;
sig6=params->sigma6;
sig12=params->sigma12;
+ if(ai<aj) return 0;
+
v3_sub(&distance,&(aj->r),&(ai->r));
if(bc) check_per_bound(moldyn,&distance);
d=v3_absolute_square(&distance); /* 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);
+ moldyn->energy+=(eps*(sig12*h1-sig6*h2)-params->uc);
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,-1.0*d); /* f = - grad E */
+ v3_scale(&force,&distance,d);
+ v3_add(&(aj->f),&(aj->f),&force);
+ v3_scale(&force,&force,-1.0); /* f = - grad E */
v3_add(&(ai->f),&(ai->f),&force);
+ virial_calc(ai,&force,&distance);
+ virial_calc(aj,&force,&distance); /* f and d signe switched */
}
return 0;
int tersoff_mult_complete_params(t_tersoff_mult_params *p) {
printf("[moldyn] tersoff parameter completion\n");
+ p->S2[0]=p->S[0]*p->S[0];
+ p->S2[1]=p->S[1]*p->S[1];
p->Smixed=sqrt(p->S[0]*p->S[1]);
+ p->S2mixed=p->Smixed*p->Smixed;
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->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(" S (A) | %f | %f | %f\n",p->S[0],p->S[1],p->Smixed);
+ printf(" R (A) | %f | %f | %f\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],
/* tersoff 1 body part */
int tersoff_mult_1bp(t_moldyn *moldyn,t_atom *ai) {
- int num;
+ int brand;
t_tersoff_mult_params *params;
t_tersoff_exchange *exchange;
- num=ai->bnum;
+ brand=ai->brand;
params=moldyn->pot1b_params;
exchange=&(params->exchange);
* their right values
*/
- exchange->beta_i=&(params->beta[num]);
- exchange->n_i=&(params->n[num]);
- exchange->c_i=&(params->c[num]);
- exchange->d_i=&(params->d[num]);
- exchange->h_i=&(params->h[num]);
+ exchange->beta_i=&(params->beta[brand]);
+ exchange->n_i=&(params->n[brand]);
+ exchange->c_i=&(params->c[brand]);
+ exchange->d_i=&(params->d[brand]);
+ exchange->h_i=&(params->h[brand]);
exchange->betaini=pow(*(exchange->beta_i),*(exchange->n_i));
- exchange->ci2=params->c[num]*params->c[num];
- exchange->di2=params->d[num]*params->d[num];
+ exchange->ci2=params->c[brand]*params->c[brand];
+ exchange->di2=params->d[brand]*params->d[brand];
exchange->ci2di2=exchange->ci2/exchange->di2;
return 0;
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 d_ij,d_ij2;
+ double A,B,R,S,S2,lambda,mu;
double f_r,df_r;
double f_c,df_c;
- int num;
+ int brand;
double s_r;
double arg;
params=moldyn->pot2b_params;
- num=aj->bnum;
+ brand=aj->brand;
exchange=&(params->exchange);
/* clear 3bp and 2bp post run */
*
*/
- /* dist_ij, d_ij */
- v3_sub(&dist_ij,&(aj->r),&(ai->r));
- if(bc) check_per_bound(moldyn,&dist_ij);
- d_ij=v3_norm(&dist_ij);
-
- /* save for use in 3bp */
- exchange->d_ij=d_ij;
- exchange->dist_ij=dist_ij;
-
/* constants */
- if(num==ai->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];
+ if(brand==ai->brand) {
+ S=params->S[brand];
+ S2=params->S2[brand];
+ R=params->R[brand];
+ A=params->A[brand];
+ B=params->B[brand];
+ lambda=params->lambda[brand];
+ mu=params->mu[brand];
exchange->chi=1.0;
}
else {
S=params->Smixed;
+ S2=params->S2mixed;
R=params->Rmixed;
A=params->Amixed;
B=params->Bmixed;
params->exchange.chi=params->chi;
}
- /* if d_ij > S => no force & potential energy contribution */
- if(d_ij>S)
+ /* dist_ij, d_ij */
+ v3_sub(&dist_ij,&(aj->r),&(ai->r));
+ if(bc) check_per_bound(moldyn,&dist_ij);
+ d_ij2=v3_absolute_square(&dist_ij);
+
+ /* if d_ij2 > S2 => no force & potential energy contribution */
+ if(d_ij2>S2)
return 0;
+ /* now we will need the distance */
+ //d_ij=v3_norm(&dist_ij);
+ d_ij=sqrt(d_ij2);
+
+ /* save for use in 3bp */
+ exchange->d_ij=d_ij;
+ exchange->d_ij2=d_ij2;
+ exchange->dist_ij=dist_ij;
+
/* more constants */
- exchange->beta_j=&(params->beta[num]);
- exchange->n_j=&(params->n[num]);
- exchange->c_j=&(params->c[num]);
- exchange->d_j=&(params->d[num]);
- exchange->h_j=&(params->h[num]);
- if(num==ai->bnum) {
+ exchange->beta_j=&(params->beta[brand]);
+ exchange->n_j=&(params->n[brand]);
+ exchange->c_j=&(params->c[brand]);
+ exchange->d_j=&(params->d[brand]);
+ exchange->h_j=&(params->h[brand]);
+ if(brand==ai->brand) {
exchange->betajnj=exchange->betaini;
exchange->cj2=exchange->ci2;
exchange->dj2=exchange->di2;
}
else {
exchange->betajnj=pow(*(exchange->beta_j),*(exchange->n_j));
- exchange->cj2=params->c[num]*params->c[num];
- exchange->dj2=params->d[num]*params->d[num];
+ exchange->cj2=params->c[brand]*params->c[brand];
+ exchange->dj2=params->d[brand]*params->d[brand];
exchange->cj2dj2=exchange->cj2/exchange->dj2;
}
/* f_a, df_a calc (again, same for ij and ji) | save for later use! */
exchange->f_a=-B*exp(-mu*d_ij);
- exchange->df_a=-mu*exchange->f_a/d_ij;
+ exchange->df_a=mu*exchange->f_a/d_ij;
/* f_c, df_c calc (again, same for ij and ji) */
if(d_ij<R) {
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));
+ df_c=0.5*sin(arg)*(M_PI/(s_r*d_ij));
/* two body contribution (ij, ji) */
v3_scale(&force,&dist_ij,-df_c*f_r-df_r*f_c);
/* tell 3bp that S > r > R */
* dVij = dVji and we sum up both: no 1/2) */
v3_add(&(ai->f),&(ai->f),&force);
+ /* virial */
+ ai->virial.xx-=force.x*dist_ij.x;
+ ai->virial.yy-=force.y*dist_ij.y;
+ ai->virial.zz-=force.z*dist_ij.z;
+ ai->virial.xy-=force.x*dist_ij.y;
+ ai->virial.xz-=force.x*dist_ij.z;
+ ai->virial.yz-=force.y*dist_ij.z;
+
+#ifdef DEBUG
+if(ai==&(moldyn->atom[0])) {
+ printf("dVij, dVji (2bp) contrib:\n");
+ printf("%f | %f\n",force.x,ai->f.x);
+ printf("%f | %f\n",force.y,ai->f.y);
+ printf("%f | %f\n",force.z,ai->f.z);
+}
+#endif
+#ifdef VDEBUG
+if(ai==&(moldyn->atom[0])) {
+ printf("dVij, dVji (2bp) contrib:\n");
+ printf("%f | %f\n",force.x*dist_ij.x,ai->virial.xx);
+ printf("%f | %f\n",force.y*dist_ij.y,ai->virial.yy);
+ printf("%f | %f\n",force.z*dist_ij.z,ai->virial.zz);
+}
+#endif
+
/* energy 2bp contribution (ij, ji) is 0.5 f_r f_c ... */
moldyn->energy+=(0.5*f_r*f_c);
zeta=exchange->zeta_ij;
if(zeta==0.0) {
moldyn->debug++; /* just for debugging ... */
- db=0.0;
b=chi;
v3_scale(&force,dist_ij,df_a*b*f_c);
}
/* add force */
v3_add(&(ai->f),&(ai->f),&force);
+ /* virial */
+ ai->virial.xx-=force.x*dist_ij->x;
+ ai->virial.yy-=force.y*dist_ij->y;
+ ai->virial.zz-=force.z*dist_ij->z;
+ ai->virial.xy-=force.x*dist_ij->y;
+ ai->virial.xz-=force.x*dist_ij->z;
+ ai->virial.yz-=force.y*dist_ij->z;
+
+#ifdef DEBUG
+if(ai==&(moldyn->atom[0])) {
+ printf("dVij (3bp) contrib:\n");
+ printf("%f | %f\n",force.x,ai->f.x);
+ printf("%f | %f\n",force.y,ai->f.y);
+ printf("%f | %f\n",force.z,ai->f.z);
+}
+#endif
+#ifdef VDEBUG
+if(ai==&(moldyn->atom[0])) {
+ printf("dVij (3bp) contrib:\n");
+ printf("%f | %f\n",force.x*dist_ij->x,ai->virial.xx);
+ printf("%f | %f\n",force.y*dist_ij->y,ai->virial.yy);
+ printf("%f | %f\n",force.z*dist_ij->z,ai->virial.zz);
+}
+#endif
+
/* add energy of 3bp sum */
moldyn->energy+=(0.5*f_c*b*f_a);
v3_scale(&force,&force,-0.5);
/* add force */
- v3_sub(&(ai->f),&(ai->f),&force);
+ v3_add(&(ai->f),&(ai->f),&force);
+
+ /* virial - plus sign, as dist_ij = - dist_ji - (really??) */
+// TEST ... with a minus instead
+ ai->virial.xx-=force.x*dist_ij->x;
+ ai->virial.yy-=force.y*dist_ij->y;
+ ai->virial.zz-=force.z*dist_ij->z;
+ ai->virial.xy-=force.x*dist_ij->y;
+ ai->virial.xz-=force.x*dist_ij->z;
+ ai->virial.yz-=force.y*dist_ij->z;
+
+#ifdef DEBUG
+if(ai==&(moldyn->atom[0])) {
+ printf("dVji (3bp) contrib:\n");
+ printf("%f | %f\n",force.x,ai->f.x);
+ printf("%f | %f\n",force.y,ai->f.y);
+ printf("%f | %f\n",force.z,ai->f.z);
+}
+#endif
+#ifdef VDEBUG
+if(ai==&(moldyn->atom[0])) {
+ printf("dVji (3bp) contrib:\n");
+ printf("%f | %f\n",force.x*dist_ij->x,ai->virial.xx);
+ printf("%f | %f\n",force.y*dist_ij->y,ai->virial.yy);
+ printf("%f | %f\n",force.z*dist_ij->z,ai->virial.zz);
+}
+#endif
return 0;
}
t_3dvec dist_ij,dist_ik,dist_jk;
t_3dvec temp1,temp2;
t_3dvec *dzeta;
- double R,S,s_r;
+ double R,S,S2,s_r;
double B,mu;
- double d_ij,d_ik,d_jk;
+ double d_ij,d_ik,d_jk,d_ij2,d_ik2,d_jk2;
double rr,dd;
double f_c,df_c;
double f_c_ik,df_c_ik,arg;
double h_cos,d2_h_cos2;
double frac,g,zeta,chi;
double tmp;
- int num;
+ int brand;
params=moldyn->pot3b_params;
exchange=&(params->exchange);
/* dist_ij, d_ij - this is < S_ij ! */
dist_ij=exchange->dist_ij;
d_ij=exchange->d_ij;
+ d_ij2=exchange->d_ij2;
/* f_c_ij, df_c_ij (same for ji) */
f_c=exchange->f_c;
/* dist_ik, d_ik */
v3_sub(&dist_ik,&(ak->r),&(ai->r));
if(bc) check_per_bound(moldyn,&dist_ik);
- d_ik=v3_norm(&dist_ik);
+ d_ik2=v3_absolute_square(&dist_ik);
/* ik constants */
- num=ai->bnum;
- if(num==ak->bnum) {
- R=params->R[num];
- S=params->S[num];
+ brand=ai->brand;
+ if(brand==ak->brand) {
+ R=params->R[brand];
+ S=params->S[brand];
+ S2=params->S2[brand];
}
else {
R=params->Rmixed;
S=params->Smixed;
+ S2=params->S2mixed;
}
/* zeta_ij/dzeta_ij contribution only for d_ik < S */
- if(d_ik<S) {
+ if(d_ik2<S2) {
+
+ /* now we need d_ik */
+ d_ik=sqrt(d_ik2);
/* get constants_i from exchange data */
n=*(exchange->n_i);
/* d_costheta */
tmp=1.0/dd;
- d_costheta1=cos_theta/(d_ij*d_ij)-tmp;
- d_costheta2=cos_theta/(d_ik*d_ik)-tmp;
+ d_costheta1=cos_theta/d_ij2-tmp;
+ d_costheta2=cos_theta/d_ik2-tmp;
/* some usefull values */
h_cos=(h-cos_theta);
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));
+ df_c_ik=0.5*sin(arg)*(M_PI/(s_r*d_ik));
/* zeta_ij */
exchange->zeta_ij+=f_c_ik*g;
/* dist_jk, d_jk */
v3_sub(&dist_jk,&(ak->r),&(aj->r));
if(bc) check_per_bound(moldyn,&dist_jk);
- d_jk=v3_norm(&dist_jk);
+ d_jk2=v3_absolute_square(&dist_jk);
/* jk constants */
- num=aj->bnum;
- if(num==ak->bnum) {
- R=params->R[num];
- S=params->S[num];
- B=params->B[num];
- mu=params->mu[num];
+ brand=aj->brand;
+ if(brand==ak->brand) {
+ R=params->R[brand];
+ S=params->S[brand];
+ S2=params->S2[brand];
+ B=params->B[brand];
+ mu=params->mu[brand];
chi=1.0;
}
else {
R=params->Rmixed;
S=params->Smixed;
+ S2=params->S2mixed;
B=params->Bmixed;
mu=params->mu_m;
chi=params->chi;
}
/* zeta_ji/dzeta_ji contribution only for d_jk < S_jk */
- if(d_jk<S) {
+ if(d_jk2<S2) {
+
+ /* now we need d_ik */
+ d_jk=sqrt(d_jk2);
/* constants_j from exchange data */
n=*(exchange->n_j);
c2d2=exchange->cj2dj2;
/* cosine of theta_jik by scalaproduct */
- rr=v3_scalar_product(&dist_ij,&dist_jk); /* times -1 */
+ rr=-v3_scalar_product(&dist_ij,&dist_jk); /* -1, as ij -> ji */
dd=d_ij*d_jk;
cos_theta=rr/dd;
/* d_costheta */
- d_costheta1=1.0/(d_jk*d_ij);
- d_costheta2=cos_theta/(d_ij*d_ij); /* in fact -cos(), but ^ */
+ d_costheta1=1.0/dd;
+ d_costheta2=cos_theta/d_ij2;
/* some usefull values */
h_cos=(h-cos_theta);
/* g(cos_theta) */
g=1.0+c2d2-frac;
- /* d_costheta_ij and dg(cos_theta) - needed in any case! */
+ /* d_costheta_jik and dg(cos_theta) - needed in any case! */
v3_scale(&temp1,&dist_jk,d_costheta1);
v3_scale(&temp2,&dist_ij,-d_costheta2); /* ji -> ij => -1 */
- v3_add(&temp1,&temp1,&temp2);
+ //v3_add(&temp1,&temp1,&temp2);
+ v3_sub(&temp1,&temp1,&temp2); /* there is a minus! */
v3_scale(&temp1,&temp1,-2.0*frac*h_cos/d2_h_cos2); /* dg */
+ /* store dg in temp2 and use it for dVjk later */
+ v3_copy(&temp2,&temp1);
+
/* f_c_jk + {d,}zeta contribution (df_c_jk = 0) */
dzeta=&(exchange->dzeta_ji);
if(d_jk<R) {
/* zeta_ji */
exchange->zeta_ji+=f_c_jk*g;
- /* dzeta_ij */
+ /* dzeta_ji */
v3_scale(&temp1,&temp1,f_c_jk);
v3_add(dzeta,dzeta,&temp1);
}
/* dV_jk stuff | add force contribution on atom i immediately */
if(exchange->d_ij_between_rs) {
zeta=f_c*g;
- v3_scale(&temp1,&temp1,f_c);
- v3_scale(&temp2,&dist_ij,df_c);
- v3_add(&temp1,&temp1,&temp2);
+ v3_scale(&temp1,&temp2,f_c);
+ v3_scale(&temp2,&dist_ij,df_c*g);
+ v3_add(&temp2,&temp2,&temp1); /* -> dzeta_jk in temp2 */
}
else {
zeta=g;
- // dzeta_jk is simply dg, which is temp1
+ // dzeta_jk is simply dg, which is stored in temp2
}
/* betajnj * zeta_jk ^ nj-1 */
tmp=exchange->betajnj*pow(zeta,(n-1.0));
- tmp=-chi/2.0*pow(1+tmp*zeta,-1.0/(2.0*n)-1)*tmp;
- v3_scale(&temp1,&temp1,tmp*B*exp(-mu*d_jk)*f_c_jk*0.5);
- v3_add(&(ai->f),&(ai->f),&temp1); /* -1 skipped in f_a calc ^ */
+ tmp=-chi/2.0*pow((1+tmp*zeta),(-1.0/(2.0*n)-1))*tmp;
+ v3_scale(&temp2,&temp2,tmp*B*exp(-mu*d_jk)*f_c_jk*0.5);
+ v3_add(&(ai->f),&(ai->f),&temp2); /* -1 skipped in f_a calc ^ */
/* scaled with 0.5 ^ */
+
+ /* virial */
+ ai->virial.xx-=temp2.x*dist_jk.x;
+ ai->virial.yy-=temp2.y*dist_jk.y;
+ ai->virial.zz-=temp2.z*dist_jk.z;
+ ai->virial.xy-=temp2.x*dist_jk.y;
+ ai->virial.xz-=temp2.x*dist_jk.z;
+ ai->virial.yz-=temp2.y*dist_jk.z;
+
+#ifdef DEBUG
+if(ai==&(moldyn->atom[0])) {
+ printf("dVjk (3bp) contrib:\n");
+ printf("%f | %f\n",temp2.x,ai->f.x);
+ printf("%f | %f\n",temp2.y,ai->f.y);
+ printf("%f | %f\n",temp2.z,ai->f.z);
+}
+#endif
+#ifdef VDEBUG
+if(ai==&(moldyn->atom[0])) {
+ printf("dVjk (3bp) contrib:\n");
+ printf("%f | %f\n",temp2.x*dist_jk.x,ai->virial.xx);
+ printf("%f | %f\n",temp2.y*dist_jk.y,ai->virial.yy);
+ printf("%f | %f\n",temp2.z*dist_jk.z,ai->virial.zz);
+}
+#endif
+
}
return 0;
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)
+ 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*1e10,dim->x/2*1e10);
+ 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*1e10,dim->y/2*1e10);
+ 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*1e10,dim->z/2*1e10);
+ i,atom[i].r.z,dim->z/2);
}
return 0;
}
-
projects / physik / posic.git / blobdiff