#include "moldyn.h"
-#include "math/math.h"
-#include "init/init.h"
-#include "random/random.h"
-#include "visual/visual.h"
-#include "list/list.h"
-
-int moldyn_usage(char **argv) {
-
- printf("\n%s usage:\n\n",argv[0]);
- printf("--- general options ---\n");
- printf("-E <steps> <file> (log total energy)\n");
- printf("-M <steps> <file> (log total momentum)\n");
- printf("-D <steps> <file> (dump total information)\n");
- printf("-S <steps> <filebase> (single save file)\n");
- printf("-V <steps> <filebase> (rasmol file)\n");
- printf("--- physics options ---\n");
- printf("-T <temperature> [K] (%f)\n",MOLDYN_TEMP);
- printf("-t <timestep tau> [s] (%.15f)\n",MOLDYN_TAU);
- printf("-C <cutoff radius> [m] (%.15f)\n",MOLDYN_CUTOFF);
- printf("-R <runs> (%d)\n",MOLDYN_RUNS);
- printf(" -- integration algo --\n");
- printf(" -I <number> (%d)\n",MOLDYN_INTEGRATE_DEFAULT);
- printf(" 0: velocity verlet\n");
- printf(" -- potential --\n");
- printf(" -P <number> <param1 param2 ...>\n");
- printf(" 0: harmonic oscillator\n");
- printf(" param1: spring constant\n");
- printf(" param2: equilibrium distance\n");
- printf(" 1: lennard jones\n");
- printf(" param1: epsilon\n");
- printf(" param2: sigma\n");
- printf("\n");
+int moldyn_init(t_moldyn *moldyn,int argc,char **argv) {
+
+ printf("[moldyn] init\n");
+
+ memset(moldyn,0,sizeof(t_moldyn));
+
+ rand_init(&(moldyn->random),NULL,1);
+ moldyn->random.status|=RAND_STAT_VERBOSE;
return 0;
}
-int moldyn_parse_argv(t_moldyn *moldyn,int argc,char **argv) {
+int moldyn_shutdown(t_moldyn *moldyn) {
- int i;
- t_ho_params hop;
- t_lj_params ljp;
- double s,e;
+ printf("[moldyn] shutdown\n");
- memset(moldyn,0,sizeof(t_moldyn));
+ moldyn_log_shutdown(moldyn);
+ link_cell_shutdown(moldyn);
+ rand_close(&(moldyn->random));
+ free(moldyn->atom);
+
+ return 0;
+}
+
+int set_int_alg(t_moldyn *moldyn,u8 algo) {
- /* default values */
- moldyn->t=MOLDYN_TEMP;
- moldyn->tau=MOLDYN_TAU;
- moldyn->time_steps=MOLDYN_RUNS;
- moldyn->integrate=velocity_verlet;
- moldyn->potential_force_function=lennard_jones;
-
- /* parse argv */
- for(i=1;i<argc;i++) {
- if(argv[i][0]=='-') {
- switch(argv[i][1]){
- case 'E':
- moldyn->ewrite=atoi(argv[++i]);
- strncpy(moldyn->efb,argv[++i],64);
- break;
- case 'M':
- moldyn->mwrite=atoi(argv[++i]);
- strncpy(moldyn->mfb,argv[++i],64);
- break;
- case 'D':
- moldyn->dwrite=atoi(argv[++i]);
- strncpy(moldyn->dfb,argv[++i],64);
- break;
- case 'S':
- moldyn->swrite=atoi(argv[++i]);
- strncpy(moldyn->sfb,argv[++i],64);
- break;
- case 'V':
- moldyn->vwrite=atoi(argv[++i]);
- strncpy(moldyn->vfb,argv[++i],64);
- break;
- case 'T':
- moldyn->t=atof(argv[++i]);
- break;
- case 't':
- moldyn->tau=atof(argv[++i]);
- break;
- case 'C':
- moldyn->cutoff=atof(argv[++i]);
- break;
- case 'R':
- moldyn->time_steps=atoi(argv[++i]);
- break;
- case 'I':
- /* integration algorithm */
- switch(atoi(argv[++i])) {
+ printf("[moldyn] integration algorithm: ");
+
+ switch(algo) {
case MOLDYN_INTEGRATE_VERLET:
moldyn->integrate=velocity_verlet;
+ printf("velocity verlet\n");
break;
default:
- printf("unknown integration algo %s\n",argv[i]);
- moldyn_usage(argv);
+ printf("unknown integration algorithm: %02x\n",algo);
+ printf("unknown\n");
return -1;
}
- case 'P':
- /* potential + params */
- switch(atoi(argv[++i])) {
- case MOLDYN_POTENTIAL_HO:
- hop.spring_constant=atof(argv[++i]);
- hop.equilibrium_distance=atof(argv[++i]);
- moldyn->pot_params=malloc(sizeof(t_ho_params));
- memcpy(moldyn->pot_params,&hop,sizeof(t_ho_params));
- moldyn->potential_force_function=harmonic_oscillator;
- break;
- case MOLDYN_POTENTIAL_LJ:
- e=atof(argv[++i]);
- s=atof(argv[++i]);
- ljp.epsilon4=4*e;
- ljp.sigma6=s*s*s*s*s*s;
- ljp.sigma12=ljp.sigma6*ljp.sigma6;
- moldyn->pot_params=malloc(sizeof(t_lj_params));
- memcpy(moldyn->pot_params,&ljp,sizeof(t_lj_params));
- moldyn->potential_force_function=lennard_jones;
- break;
- default:
- printf("unknown potential %s\n",argv[i]);
- moldyn_usage(argv);
- return -1;
- }
+ return 0;
+}
- default:
- printf("unknown option %s\n",argv[i]);
- moldyn_usage(argv);
- return -1;
- }
- } else {
- moldyn_usage(argv);
- return -1;
- }
- }
+int set_cutoff(t_moldyn *moldyn,double cutoff) {
+
+ moldyn->cutoff=cutoff;
+
+ printf("[moldyn] cutoff [A]: %f\n",moldyn->cutoff);
return 0;
}
-int moldyn_log_init(t_moldyn *moldyn) {
+int set_temperature(t_moldyn *moldyn,double t_ref) {
- moldyn->lvstat=0;
- t_visual *vis;
+ moldyn->t_ref=t_ref;
- vis=&(moldyn->vis);
+ printf("[moldyn] temperature: %f\n",moldyn->t_ref);
- if(moldyn->ewrite) {
- moldyn->efd=open(moldyn->efb,O_WRONLY|O_CREAT|O_TRUNC);
- if(moldyn->efd<0) {
- perror("[moldyn] efd open");
- return moldyn->efd;
- }
- dprintf(moldyn->efd,"# moldyn total energy logfile\n");
- moldyn->lvstat|=MOLDYN_LVSTAT_TOTAL_E;
- }
+ return 0;
+}
- if(moldyn->mwrite) {
- moldyn->mfd=open(moldyn->mfb,O_WRONLY|O_CREAT|O_TRUNC);
- if(moldyn->mfd<0) {
- perror("[moldyn] mfd open");
- return moldyn->mfd;
- }
- dprintf(moldyn->mfd,"# moldyn total momentum logfile\n");
- moldyn->lvstat|=MOLDYN_LVSTAT_TOTAL_M;
- }
+int set_pressure(t_moldyn *moldyn,double p_ref) {
- if(moldyn->swrite)
- moldyn->lvstat|=MOLDYN_LVSTAT_SAVE;
+ moldyn->p_ref=p_ref;
- if(moldyn->dwrite) {
- moldyn->dfd=open(moldyn->dfb,O_WRONLY|O_CREAT|O_TRUNC);
- if(moldyn->dfd<0) {
- perror("[moldyn] dfd open");
- return moldyn->dfd;
- }
- write(moldyn->dfd,moldyn,sizeof(t_moldyn));
- moldyn->lvstat|=MOLDYN_LVSTAT_DUMP;
- }
+ printf("[moldyn] pressure: %f\n",moldyn->p_ref);
+
+ return 0;
+}
+
+int set_pt_scale(t_moldyn *moldyn,u8 ptype,double ptc,u8 ttype,double ttc) {
+
+ moldyn->pt_scale=(ptype|ttype);
+ 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");
- if((moldyn->vwrite)&&(vis)) {
- moldyn->visual=vis;
- visual_init(vis,moldyn->vfb);
- moldyn->lvstat|=MOLDYN_LVSTAT_VISUAL;
+ printf(" t: %s",ttype?"yes":"no ");
+ if(ttype)
+ printf(" | type: %02x | factor: %f",ttype,ttc);
+ printf("\n");
+
+ return 0;
+}
+
+int set_dim(t_moldyn *moldyn,double x,double y,double z,u8 visualize) {
+
+ moldyn->dim.x=x;
+ 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->lvstat|=MOLDYN_LVSTAT_INITIALIZED;
+ 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 moldyn_log_shutdown(t_moldyn *moldyn) {
+int set_nn_dist(t_moldyn *moldyn,double dist) {
- if(moldyn->efd) close(moldyn->efd);
- if(moldyn->mfd) close(moldyn->efd);
- if(moldyn->dfd) close(moldyn->efd);
- if(moldyn->visual) visual_tini(moldyn->visual);
+ moldyn->nnd=dist;
return 0;
}
-int moldyn_init(t_moldyn *moldyn,int argc,char **argv) {
+int set_pbc(t_moldyn *moldyn,u8 x,u8 y,u8 z) {
- int ret;
+ printf("[moldyn] periodic boundary conditions:\n");
- ret=moldyn_parse_argv(moldyn,argc,argv);
- if(ret<0) return ret;
+ if(x)
+ moldyn->status|=MOLDYN_STAT_PBX;
- ret=moldyn_log_init(moldyn);
- if(ret<0) return ret;
+ if(y)
+ moldyn->status|=MOLDYN_STAT_PBY;
- rand_init(&(moldyn->random),NULL,1);
- moldyn->random.status|=RAND_STAT_VERBOSE;
+ if(z)
+ moldyn->status|=MOLDYN_STAT_PBZ;
- moldyn->status=0;
+ printf(" x: %s\n",x?"yes":"no");
+ printf(" y: %s\n",y?"yes":"no");
+ printf(" z: %s\n",z?"yes":"no");
return 0;
}
-int moldyn_shutdown(t_moldyn *moldyn) {
+int set_potential1b(t_moldyn *moldyn,pf_func1b func,void *params) {
- moldyn_log_shutdown(moldyn);
- rand_close(&(moldyn->random));
- free(moldyn->atom);
+ moldyn->func1b=func;
+ moldyn->pot1b_params=params;
return 0;
}
-int create_lattice(unsigned char type,int element,double mass,double lc,
- int a,int b,int c,t_atom **atom) {
+int set_potential2b(t_moldyn *moldyn,pf_func2b func,void *params) {
- int count;
+ moldyn->func2b=func;
+ moldyn->pot2b_params=params;
+
+ return 0;
+}
+
+int set_potential2b_post(t_moldyn *moldyn,pf_func2b_post func,void *params) {
+
+ moldyn->func2b_post=func;
+ moldyn->pot2b_params=params;
+
+ return 0;
+}
+
+int set_potential3b(t_moldyn *moldyn,pf_func3b func,void *params) {
+
+ moldyn->func3b=func;
+ moldyn->pot3b_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) {
+
+ 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;
+ 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] 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;
+ 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] 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;
+ printf("save file (%d)\n",timer);
+ break;
+ case VISUAL_STEP:
+ moldyn->vwrite=timer;
+ 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 type: %02x\n",type);
+ return -1;
+ }
+
+ return 0;
+}
+
+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 brand,int a,int b,int c) {
+
+ int new,count;
int ret;
t_3dvec origin;
+ void *ptr;
+ t_atom *atom;
- count=a*b*c;
+ new=a*b*c;
+ count=moldyn->count;
- if(type==FCC) count*=4;
- 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;
- *atom=malloc(count*sizeof(t_atom));
- if(*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:
+ ret=cubic_init(a,b,c,lc,atom,NULL);
+ break;
case FCC:
- ret=fcc_init(a,b,c,lc,*atom,&origin);
+ ret=fcc_init(a,b,c,lc,atom,NULL);
break;
case DIAMOND:
- ret=diamond_init(a,b,c,lc,*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;
}
- while(count) {
- (*atom)[count-1].element=element;
- (*atom)[count-1].mass=mass;
- count-=1;
+ moldyn->count+=new;
+ printf("[moldyn] created lattice with %d atoms\n",new);
+
+ for(ret=0;ret<new;ret++) {
+ atom[ret].element=element;
+ atom[ret].mass=mass;
+ atom[ret].attr=attr;
+ atom[ret].brand=brand;
+ atom[ret].tag=count+ret;
+ check_per_bound(moldyn,&(atom[ret].r));
}
return ret;
}
-int destroy_lattice(t_atom *atom) {
+/* 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++) {
+ for(k=0;k<c;k++) {
+ r.z=o.z;
+ 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;
+ 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(atom) free(atom);
+ if(moldyn->atom) free(moldyn->atom);
return 0;
}
-int thermal_init(t_moldyn *moldyn) {
+int thermal_init(t_moldyn *moldyn,u8 equi_init) {
/*
* - gaussian distribution of velocities
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++) {
- sigma=sqrt(2.0*K_BOLTZMANN*moldyn->t/atom[i].mass);
+ sigma=sqrt(2.0*K_BOLTZMANN*moldyn->t_ref/atom[i].mass);
/* x direction */
v=sigma*rand_get_gauss(random);
atom[i].v.x=v;
}
/* velocity scaling */
- scale_velocity(moldyn);
+ scale_velocity(moldyn,equi_init);
return 0;
}
-int scale_velocity(t_moldyn *moldyn) {
+double temperature_calc(t_moldyn *moldyn) {
+ double double_ekin;
int i;
- double e,c;
t_atom *atom;
atom=moldyn->atom;
- /*
- * - velocity scaling (E = 3/2 N k T), E: kinetic energy
- */
- e=0.0;
+ double_ekin=0;
for(i=0;i<moldyn->count;i++)
- e+=0.5*atom[i].mass*v3_absolute_square(&(atom[i].v));
- c=sqrt((2.0*e)/(3.0*moldyn->count*K_BOLTZMANN*moldyn->t));
- for(i=0;i<moldyn->count;i++)
- v3_scale(&(atom[i].v),&(atom[i].v),(1.0/c));
+ double_ekin+=atom[i].mass*v3_absolute_square(&(atom[i].v));
- return 0;
+ /* kinetic energy = 3/2 N k_B T */
+ moldyn->t=double_ekin/(3.0*K_BOLTZMANN*moldyn->count);
+
+ return moldyn->t;
+}
+
+double get_temperature(t_moldyn *moldyn) {
+
+ return moldyn->t;
}
-double get_e_kin(t_atom *atom,int count) {
+int scale_velocity(t_moldyn *moldyn,u8 equi_init) {
int i;
- double e;
+ double e,scale;
+ t_atom *atom;
+ int count;
- e=0.0;
+ atom=moldyn->atom;
- for(i=0;i<count;i++) {
- e+=0.5*atom[i].mass*v3_absolute_square(&(atom[i].v));
+ /*
+ * - velocity scaling (E = 3/2 N k T), E: kinetic energy
+ */
+
+ /* get kinetic energy / temperature & count involved atoms */
+ e=0.0;
+ count=0;
+ for(i=0;i<moldyn->count;i++) {
+ if((equi_init&TRUE)||(atom[i].attr&ATOM_ATTR_HB)) {
+ e+=atom[i].mass*v3_absolute_square(&(atom[i].v));
+ count+=1;
+ }
+ }
+ 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) {
+ thermal_init(moldyn,equi_init);
+ return 0;
+ }
+ else
+ return 0; /* no scaling needed */
}
- return e;
-}
-double get_e_pot(t_moldyn *moldyn) {
+ /* get scaling factor */
+ scale=moldyn->t_ref/moldyn->t;
+ if(equi_init&TRUE)
+ scale*=2.0;
+ else
+ if(moldyn->pt_scale&T_SCALE_BERENDSEN)
+ scale=1.0+(scale-1.0)/moldyn->t_tc;
+ scale=sqrt(scale);
+
+ /* velocity scaling */
+ 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 moldyn->energy;
+ return 0;
}
-double get_total_energy(t_moldyn *moldyn) {
+double ideal_gas_law_pressure(t_moldyn *moldyn) {
- double e;
+ double p;
- e=get_e_kin(moldyn->atom,moldyn->count);
- e+=get_e_pot(moldyn);
+ p=moldyn->count*moldyn->t*K_BOLTZMANN/moldyn->volume;
- return e;
+ return p;
}
-t_3dvec get_total_p(t_atom *atom, int count) {
+double pressure_calc(t_moldyn *moldyn) {
- t_3dvec p,p_total;
int i;
+ double v;
+ t_virial *virial;
- v3_zero(&p_total);
- for(i=0;i<count;i++) {
- v3_scale(&p,&(atom[i].v),atom[i].mass);
- v3_add(&p_total,&p_total,&p);
+ v=0.0;
+ for(i=0;i<moldyn->count;i++) {
+ virial=&(moldyn->atom[i].virial);
+ v+=(virial->xx+virial->yy+virial->zz);
}
+ v*=ONE_THIRD;
+printf("kieck mal: %f %f %f\n",v,moldyn->count*K_BOLTZMANN*moldyn->t,v/moldyn->count);
- return p_total;
-}
+ moldyn->p=moldyn->count*K_BOLTZMANN*moldyn->t+v;
+ moldyn->p/=moldyn->volume;
-double estimate_time_step(t_moldyn *moldyn,double nn_dist,double t) {
+ return moldyn->p;
+}
- double tau;
+double thermodynamic_pressure_calc(t_moldyn *moldyn) {
- tau=0.05*nn_dist/(sqrt(3.0*K_BOLTZMANN*t/moldyn->atom[0].mass));
- tau*=1.0E-9;
- if(tau<moldyn->tau)
- printf("[moldyn] warning: time step (%f > %.15f)\n",
- moldyn->tau,tau);
+ t_3dvec dim,*tp;
+ double u,p;
+ double scale;
+ t_atom *store;
- return tau;
-}
+ tp=&(moldyn->tp);
+ store=malloc(moldyn->count*sizeof(t_atom));
+ if(store==NULL) {
+ printf("[moldyn] allocating store mem failed\n");
+ return -1;
+ }
-/*
- * numerical tricks
- */
+ /* 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;
-/* linked list / cell method */
+ link_cell_shutdown(moldyn);
+ link_cell_init(moldyn);
-int link_cell_init(t_moldyn *moldyn) {
+ return sqrt(p);
+}
- t_linkcell *lc;
- int i;
+double get_pressure(t_moldyn *moldyn) {
- lc=&(moldyn->lc);
+ return moldyn->p;
- /* list log fd */
- lc->listfd=open("/dev/null",O_WRONLY);
+}
- /* partitioning the md cell */
- lc->nx=moldyn->dim.x/moldyn->cutoff;
- lc->x=moldyn->dim.x/lc->nx;
- lc->ny=moldyn->dim.y/moldyn->cutoff;
- lc->y=moldyn->dim.y/lc->ny;
- lc->nz=moldyn->dim.z/moldyn->cutoff;
- lc->z=moldyn->dim.z/lc->nz;
+int scale_dim(t_moldyn *moldyn,double scale,u8 x,u8 y,u8 z) {
- lc->cells=lc->nx*lc->ny*lc->nz;
- lc->subcell=malloc(lc->cells*sizeof(t_list));
+ t_3dvec *dim;
- printf("initializing linked cells (%d)\n",lc->cells);
+ dim=&(moldyn->dim);
- for(i=0;i<lc->cells;i++)
- list_init(&(lc->subcell[i]),1);
- //list_init(&(lc->subcell[i]),lc->listfd);
+ if(x) dim->x*=scale;
+ if(y) dim->y*=scale;
+ if(z) dim->z*=scale;
- link_cell_update(moldyn);
-
return 0;
}
-int link_cell_update(t_moldyn *moldyn) {
+int scale_atoms(t_moldyn *moldyn,double scale,u8 x,u8 y,u8 z) {
- int count,i,j,k;
- int nx,ny,nz;
- t_atom *atom;
- t_linkcell *lc;
+ int i;
+ t_3dvec *r;
- atom=moldyn->atom;
- lc=&(moldyn->lc);
+ 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) {
+
+ 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 update_e_kin(t_moldyn *moldyn) {
+
+ return(get_e_kin(moldyn));
+}
+
+double get_total_energy(t_moldyn *moldyn) {
+
+ return(moldyn->ekin+moldyn->energy);
+}
+
+t_3dvec get_total_p(t_moldyn *moldyn) {
+
+ t_3dvec p,p_total;
+ int i;
+ t_atom *atom;
+
+ atom=moldyn->atom;
+
+ v3_zero(&p_total);
+ for(i=0;i<moldyn->count;i++) {
+ v3_scale(&p,&(atom[i].v),atom[i].mass);
+ v3_add(&p_total,&p_total,&p);
+ }
+
+ return p_total;
+}
+
+double estimate_time_step(t_moldyn *moldyn,double nn_dist) {
+
+ double tau;
+
+ /* nn_dist is the nearest neighbour distance */
+
+ tau=(0.05*nn_dist*moldyn->atom[0].mass)/sqrt(3.0*K_BOLTZMANN*moldyn->t);
+
+ return tau;
+}
+
+/*
+ * numerical tricks
+ */
+
+/* linked list / cell method */
+
+int link_cell_init(t_moldyn *moldyn) {
+
+ t_linkcell *lc;
+ int i;
+
+ lc=&(moldyn->lc);
+
+ /* partitioning the md cell */
+ lc->nx=moldyn->dim.x/moldyn->cutoff;
+ lc->x=moldyn->dim.x/lc->nx;
+ lc->ny=moldyn->dim.y/moldyn->cutoff;
+ lc->y=moldyn->dim.y/lc->ny;
+ lc->nz=moldyn->dim.z/moldyn->cutoff;
+ lc->z=moldyn->dim.z/lc->nz;
+
+ lc->cells=lc->nx*lc->ny*lc->nz;
+ 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_f(&(lc->subcell[i]));
+
+ link_cell_update(moldyn);
+
+ return 0;
+}
+
+int link_cell_update(t_moldyn *moldyn) {
+
+ int count,i,j,k;
+ int nx,ny;
+ t_atom *atom;
+ t_linkcell *lc;
+ 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;
int ci,cj,ck;
int nx,ny,nz;
int x,y,z;
- unsigned char bx,by,bz;
+ u8 bx,by,bz;
lc=&(moldyn->lc);
nx=lc->nx;
count2=27;
a=nx*ny;
-
cell[0]=lc->subcell[i+j*nx+k*a];
- printf("%d\n",i+j*nx+k*a);
for(ci=-1;ci<=1;ci++) {
bx=0;
x=i+ci;
bz=1;
}
if(!(ci|cj|ck)) continue;
- printf(" %d %d %d \n",x,y,z);
if(bx|by|bz) {
cell[--count2]=lc->subcell[x+y*nx+z*a];
- printf("%d\n",x+y*nx+z*a);
- printf("--- %d\n",count2);
}
else {
cell[count1++]=lc->subcell[x+y*nx+z*a];
- printf("%d\n",x+y*nx+z*a);
- printf("--- %d\n",count1);
}
}
}
}
- return count2;
+ lc->dnlc=count1;
+
+ 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]));
- if(lc->listfd) close(lc->listfd);
+ free(lc->subcell);
return 0;
}
+int moldyn_add_schedule(t_moldyn *moldyn,int runs,double tau) {
+
+ int count;
+ void *ptr;
+ t_moldyn_schedule *schedule;
+
+ schedule=&(moldyn->schedule);
+ count=++(schedule->total_sched);
+
+ ptr=realloc(schedule->runs,count*sizeof(int));
+ if(!ptr) {
+ perror("[moldyn] realloc (runs)");
+ return -1;
+ }
+ schedule->runs=ptr;
+ schedule->runs[count-1]=runs;
+
+ ptr=realloc(schedule->tau,count*sizeof(double));
+ if(!ptr) {
+ perror("[moldyn] realloc (tau)");
+ return -1;
+ }
+ 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,set_hook hook,void *hook_params) {
+
+ moldyn->schedule.hook=hook;
+ moldyn->schedule.hook_params=hook_params;
+
+ return 0;
+}
+
/*
*
* 'integration of newtons equation' - algorithms
int moldyn_integrate(t_moldyn *moldyn) {
int i;
- unsigned int e,m,s,d,v;
+ unsigned int e,m,s,v;
t_3dvec p;
-
+ t_moldyn_schedule *sched;
+ t_atom *atom;
int fd;
- char fb[128];
+ char dir[128];
+ double ds;
+ double energy_scale;
+
+ sched=&(moldyn->schedule);
+ atom=moldyn->atom;
+
+ /* initialize linked cell method */
+ link_cell_init(moldyn);
/* logging & visualization */
e=moldyn->ewrite;
m=moldyn->mwrite;
s=moldyn->swrite;
- d=moldyn->dwrite;
v=moldyn->vwrite;
- if(!(moldyn->lvstat&MOLDYN_LVSTAT_INITIALIZED)) {
- printf("[moldyn] warning, lv system not initialized\n");
- return -1;
- }
-
/* 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 */
- moldyn->potential_force_function(moldyn);
+ potential_force_calc(moldyn);
- for(i=0;i<moldyn->time_steps;i++) {
+ /* 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)
+ printf("[moldyn] warning: cutoff > 0.5 x dim.y\n");
+ if(moldyn->cutoff>0.5*moldyn->dim.z)
+ printf("[moldyn] warning: cutoff > 0.5 x dim.z\n");
+ ds=0.5*atom[0].f.x*moldyn->tau_square/atom[0].mass;
+ if(ds>0.05*moldyn->nnd)
+ printf("[moldyn] warning: forces too high / tau too small!\n");
+
+ /* zero absolute time */
+ moldyn->time=0.0;
- /* neighbour list update */
- link_cell_update(moldyn);
+ /* 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=sched->tau[sched->count];
+ moldyn->tau_square=moldyn->tau*moldyn->tau;
+ moldyn->time_steps=sched->runs[sched->count];
+
+ /* integration according to schedule */
+
+ for(i=0;i<moldyn->time_steps;i++) {
/* integration step */
moldyn->integrate(moldyn);
+ /* 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);
+
+ temperature_calc(moldyn);
+ pressure_calc(moldyn);
+ //thermodynamic_pressure_calc(moldyn);
+
/* check for log & visualization */
if(e) {
if(!(i%e))
+ update_e_kin(moldyn);
dprintf(moldyn->efd,
- "%.15f %.45f\n",i*moldyn->tau,
- 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->atom,moldyn->count);
+ p=get_total_p(moldyn);
dprintf(moldyn->mfd,
- "%.15f %.45f\n",i*moldyn->tau,
- 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));
write(fd,moldyn->atom,
moldyn->count*sizeof(t_atom));
}
+ close(fd);
}
}
- if(d) {
- if(!(i%d))
- write(moldyn->dfd,moldyn->atom,
- moldyn->count*sizeof(t_atom));
-
- }
if(v) {
if(!(i%v)) {
- visual_atoms(moldyn->visual,i*moldyn->tau,
+ visual_atoms(&(moldyn->vis),moldyn->time,
moldyn->atom,moldyn->count);
- printf("\rsteps: %d",i);
+ printf("\rsched: %d, steps: %d, debug: %f | %f",
+ sched->count,i,moldyn->p/ATM,moldyn->debug/ATM);
fflush(stdout);
}
}
+
+ /* increase absolute time */
+ moldyn->time+=moldyn->tau;
+
+ }
+
+ /* check for hooks */
+ if(sched->hook)
+ sched->hook(moldyn,sched->hook_params);
+
+ /* get a new info line */
+ printf("\n");
+
}
return 0;
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);
- v3_per_bound(&(atom[i].r),&(moldyn->dim));
+ 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);
}
+ /* neighbour list update */
+ link_cell_update(moldyn);
+
/* forces depending on chosen potential */
- moldyn->potential_force_function(moldyn);
+ 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
*
*/
-/* harmonic oscillator potential and force */
+/* generic potential and force calculation */
-int harmonic_oscillator(t_moldyn *moldyn) {
+int potential_force_calc(t_moldyn *moldyn) {
- t_ho_params *params;
- t_atom *atom,*btom;
+ int i,j,k,count;
+ t_atom *itom,*jtom,*ktom;
+ t_virial *virial;
t_linkcell *lc;
- t_list *this,neighbour[27];
- int i,j,c;
- int count;
- t_3dvec force,distance;
- double d,u;
- double sc,equi_dist;
- int ni,nj,nk;
+ t_list neighbour_i[27];
+ t_list neighbour_i2[27];
+ t_list *this,*that;
+ u8 bc_ij,bc_ik;
+ int dnlc;
- params=moldyn->pot_params;
- atom=moldyn->atom;
- lc=&(moldyn->lc);
- sc=params->spring_constant;
- equi_dist=params->equilibrium_distance;
count=moldyn->count;
+ itom=moldyn->atom;
+ lc=&(moldyn->lc);
+
+ /* reset energy */
+ moldyn->energy=0.0;
+
+ /* 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;
+
+ }
- u=0.0;
+ /* get energy,force and virial of every atom */
for(i=0;i<count;i++) {
- /* determine cell + neighbours */
- ni=(atom[i].r.x+(moldyn->dim.x/2))/lc->x;
- nj=(atom[i].r.y+(moldyn->dim.y/2))/lc->y;
- nk=(atom[i].r.z+(moldyn->dim.z/2))/lc->z;
- printf("%d %d %d\n",ni,nj,nk);
- c=link_cell_neighbour_index(moldyn,ni,nj,nk,neighbour);
-
- /* processing cell of atom i */
- this=&(neighbour[0]);
- list_reset(this); /* list has 1 element at minimum */
- do {
- btom=this->current->data;
- if(btom==&(atom[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 */
+
+ 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;
+
+ for(j=0;j<27;j++) {
+
+ this=&(neighbour_i[j]);
+ list_reset_f(this);
+
+ if(this->start==NULL)
continue;
- v3_sub(&distance,&(atom[i].r),&(btom->r));
- d=v3_norm(&distance);
- u+=(0.5*sc*(d-equi_dist)*(d-equi_dist));
- v3_scale(&force,&distance,-sc*(1.0-(equi_dist/d)));
- v3_add(&(atom[i].f),&(atom[i].f),&force);
- } while(list_next(this)!=L_NO_NEXT_ELEMENT);
-
- /* neighbours not doing boundary condition overflow */
- for(j=1;j<c;j++) {
- this=&(neighbour[j]);
- list_reset(this); /* there might not be a single atom */
- if(this->start!=NULL) {
+
+ bc_ij=(j<dnlc)?0:1;
do {
- btom=this->current->data;
- v3_sub(&distance,&(atom[i].r),&(btom->r));
- d=v3_norm(&distance);
- if(d<=moldyn->cutoff) {
- u+=(0.5*sc*(d-equi_dist)*(d-equi_dist));
- v3_scale(&force,&distance,
- -sc*(1.0-(equi_dist/d)));
- v3_add(&(atom[i].f),&(atom[i].f),
- &force);
+ 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(this)!=L_NO_NEXT_ELEMENT);
- }
- }
+ /* 3 body potential/force */
- /* neighbours due to boundary conditions */
- for(j=c;j<27;j++) {
- this=&(neighbour[j]);
- list_reset(this); /* check boundary conditions */
- if(this->start!=NULL) {
+ 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));
+
+ /* get neighbours of i */
+ for(k=0;k<27;k++) {
+
+ that=&(neighbour_i2[k]);
+ list_reset_f(that);
+
+ if(that->start==NULL)
+ continue;
+
+ bc_ik=(k<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_ik|bc_ij);
+
+ } while(list_next_f(that)!=\
+ L_NO_NEXT_ELEMENT);
- do {
- btom=this->current->data;
- v3_sub(&distance,&(atom[i].r),&(btom->r));
- v3_per_bound(&distance,&(moldyn->dim));
- d=v3_norm(&distance);
- if(d<=moldyn->cutoff) {
- u+=(0.5*sc*(d-equi_dist)*(d-equi_dist));
- v3_scale(&force,&distance,
- -sc*(1.0-(equi_dist/d)));
- v3_add(&(atom[i].f),&(atom[i].f),
- &force);
}
- } 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);
+
}
+
}
- moldyn->energy=u;
+#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
+ */
+
+inline int check_per_bound(t_moldyn *moldyn,t_3dvec *a) {
+
+ double x,y,z;
+ t_3dvec *dim;
+
+ dim=&(moldyn->dim);
+
+ 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;
+ 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;
+ }
+
+ return 0;
+}
+
+
+/*
+ * example potentials
+ */
+
+/* harmonic oscillator potential and force */
+
+int harmonic_oscillator(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
+
+ t_ho_params *params;
+ t_3dvec force,distance;
+ 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) {
+ moldyn->energy+=(0.5*sc*(d-equi_dist)*(d-equi_dist));
+ /* f = -grad E; grad r_ij = -1 1/r_ij distance */
+ 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;
}
/* lennard jones potential & force for one sort of atoms */
-int lennard_jones(t_moldyn *moldyn) {
+int lennard_jones(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
t_lj_params *params;
- t_atom *atom,*btom;
- t_linkcell *lc;
- t_list *this,neighbour[27];
- int i,j,c;
- int count;
t_3dvec force,distance;
- double d,h1,h2,u;
+ double d,h1,h2;
double eps,sig6,sig12;
- int ni,nj,nk;
- params=moldyn->pot_params;
- atom=moldyn->atom;
- lc=&(moldyn->lc);
- count=moldyn->count;
+ params=moldyn->pot2b_params;
eps=params->epsilon4;
sig6=params->sigma6;
sig12=params->sigma12;
- u=0.0;
- for(i=0;i<count;i++) {
- /* determine cell + neighbours */
- ni=(atom[i].r.x+(moldyn->dim.x/2))/lc->x;
- nj=(atom[i].r.y+(moldyn->dim.y/2))/lc->y;
- nk=(atom[i].r.z+(moldyn->dim.z/2))/lc->z;
- printf("hier atom = %08x\n",&(atom[i]));
- c=link_cell_neighbour_index(moldyn,ni,nj,nk,neighbour);
- printf("da atom = %08x\n",&(atom[i]));
- printf("da atom = %08x\n",&(moldyn->atom[i]));
-
- printf("c = %d (%d %d %d)\n",c,ni,nj,nk);
-
- /* processing cell of atom i */
- this=&(neighbour[0]);
- list_reset(this); /* list has 1 element at minimum */
- do {
- btom=this->current->data;
- if(btom==&(atom[i]))
- continue;
- puts("foo");
- v3_sub(&distance,&(atom[i].r),&(btom->r));
- puts("foo");
- d=1.0/v3_absolute_square(&distance); /* 1/r^2 */
- h1=d*d; /* 1/r^4 */
- h2*=d; /* 1/r^6 */
- h1=h2*h2; /* 1/r^12 */
- u+=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(&(atom[i].f),&(atom[i].f),&force);
- printf("test!!\n");
- } while(list_next(this)!=L_NO_NEXT_ELEMENT);
-
- /* neighbours not doing boundary condition overflow */
- for(j=1;j<c;j++) {
- this=&(neighbour[j]);
- list_reset(this); /* there might not be a single atom */
- if(this->start!=NULL) {
+ 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 */
+ 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 */
+ 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,d);
+ v3_add(&(aj->f),&(aj->f),&force);
+ v3_scale(&force,&distance,-1.0*d); /* 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 */
+ }
- do {
- printf("in bound: %d\n",j);
- btom=this->current->data;
- v3_sub(&distance,&(atom[i].r),&(btom->r));
- d=v3_absolute_square(&distance); /* r^2 */
- if(d<=moldyn->cutoff_square) {
- d=1.0/d; /* 1/r^2 */
- h1=d*d; /* 1/r^4 */
- h2*=d; /* 1/r^6 */
- h1=h2*h2; /* 1/r^12 */
- u+=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(&(atom[i].f),&(atom[i].f),
- &force);
- }
- } while(list_next(this)!=L_NO_NEXT_ELEMENT);
-
- }
+ return 0;
+}
+
+/*
+ * 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->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->lambda_m=0.5*(p->lambda[0]+p->lambda[1]);
+ p->mu_m=0.5*(p->mu[0]+p->mu[1]);
+
+ printf("[moldyn] tersoff mult parameter info:\n");
+ printf(" S (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],
+ p->lambda_m);
+ printf(" mu | %f | %f | %f\n",p->mu[0],p->mu[1],p->mu_m);
+ printf(" beta | %.10f | %.10f\n",p->beta[0],p->beta[1]);
+ printf(" n | %f | %f\n",p->n[0],p->n[1]);
+ printf(" c | %f | %f\n",p->c[0],p->c[1]);
+ printf(" d | %f | %f\n",p->d[0],p->d[1]);
+ printf(" h | %f | %f\n",p->h[0],p->h[1]);
+ printf(" chi | %f \n",p->chi);
+
+ return 0;
+}
+
+/* tersoff 1 body part */
+int tersoff_mult_1bp(t_moldyn *moldyn,t_atom *ai) {
+
+ int brand;
+ t_tersoff_mult_params *params;
+ t_tersoff_exchange *exchange;
+
+ brand=ai->brand;
+ params=moldyn->pot1b_params;
+ exchange=&(params->exchange);
+
+ /*
+ * simple: point constant parameters only depending on atom i to
+ * their right values
+ */
+
+ 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[brand]*params->c[brand];
+ exchange->di2=params->d[brand]*params->d[brand];
+ exchange->ci2di2=exchange->ci2/exchange->di2;
+
+ 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,d_ij2;
+ double A,B,R,S,S2,lambda,mu;
+ double f_r,df_r;
+ double f_c,df_c;
+ int brand;
+ double s_r;
+ double arg;
+
+ params=moldyn->pot2b_params;
+ brand=aj->brand;
+ exchange=&(params->exchange);
+
+ /* clear 3bp and 2bp post run */
+ exchange->run3bp=0;
+ exchange->run2bp_post=0;
+
+ /* reset S > r > R mark */
+ exchange->d_ij_between_rs=0;
+
+ /*
+ * calc of 2bp contribution of V_ij and dV_ij/ji
+ *
+ * for Vij and dV_ij we need:
+ * - f_c_ij, df_c_ij
+ * - f_r_ij, df_r_ij
+ *
+ * for dV_ji we need:
+ * - f_c_ji = f_c_ij, df_c_ji = df_c_ij
+ * - f_r_ji = f_r_ij; df_r_ji = df_r_ij
+ *
+ */
+
+ /* constants */
+ 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;
+ lambda=params->lambda_m;
+ mu=params->mu_m;
+ params->exchange.chi=params->chi;
+ }
+
+ /* 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[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;
+ exchange->cj2dj2=exchange->ci2di2;
+ }
+ else {
+ exchange->betajnj=pow(*(exchange->beta_j),*(exchange->n_j));
+ exchange->cj2=params->c[brand]*params->c[brand];
+ exchange->dj2=params->d[brand]*params->d[brand];
+ exchange->cj2dj2=exchange->cj2/exchange->dj2;
+ }
+
+ /* f_r_ij = f_r_ji, df_r_ij = df_r_ji */
+ f_r=A*exp(-lambda*d_ij);
+ df_r=lambda*f_r/d_ij;
+
+ /* 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;
+
+ /* f_c, df_c calc (again, same for ij and ji) */
+ if(d_ij<R) {
+ /* f_c = 1, df_c = 0 */
+ f_c=1.0;
+ df_c=0.0;
+ /* two body contribution (ij, ji) */
+ 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));
+ /* two body contribution (ij, ji) */
+ v3_scale(&force,&dist_ij,-df_c*f_r-df_r*f_c);
+ /* tell 3bp that S > r > R */
+ exchange->d_ij_between_rs=1;
+ }
+
+ /* add forces of 2bp (ij, ji) contribution
+ * 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);
+
+ /* save for use in 3bp */
+ exchange->f_c=f_c;
+ exchange->df_c=df_c;
+
+ /* enable the run of 3bp function and 2bp post processing */
+ exchange->run3bp=1;
+ exchange->run2bp_post=1;
+
+ /* reset 3bp sums */
+ exchange->zeta_ij=0.0;
+ exchange->zeta_ji=0.0;
+ v3_zero(&(exchange->dzeta_ij));
+ v3_zero(&(exchange->dzeta_ji));
+
+ return 0;
+}
+
+/* tersoff 2 body post part */
+
+int tersoff_mult_post_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
+
+ /*
+ * here we have to allow for the 3bp sums
+ *
+ * that is:
+ * - zeta_ij, dzeta_ij
+ * - zeta_ji, dzeta_ji
+ *
+ * to compute the 3bp contribution to:
+ * - Vij, dVij
+ * - dVji
+ *
+ */
+
+ t_tersoff_mult_params *params;
+ t_tersoff_exchange *exchange;
+
+ t_3dvec force,temp;
+ t_3dvec *dist_ij;
+ double b,db,tmp;
+ double f_c,df_c,f_a,df_a;
+ double chi,ni,betaini,nj,betajnj;
+ double zeta;
+
+ params=moldyn->pot2b_params;
+ exchange=&(params->exchange);
+
+ /* we do not run if f_c_ij was detected to be 0! */
+ if(!(exchange->run2bp_post))
+ return 0;
+
+ f_c=exchange->f_c;
+ df_c=exchange->df_c;
+ f_a=exchange->f_a;
+ df_a=exchange->df_a;
+ betaini=exchange->betaini;
+ betajnj=exchange->betajnj;
+ ni=*(exchange->n_i);
+ nj=*(exchange->n_j);
+ chi=exchange->chi;
+ dist_ij=&(exchange->dist_ij);
+
+ /* Vij and dVij */
+ zeta=exchange->zeta_ij;
+ if(zeta==0.0) {
+ moldyn->debug++; /* just for debugging ... */
+ b=chi;
+ v3_scale(&force,dist_ij,df_a*b*f_c);
+ }
+ else {
+ tmp=betaini*pow(zeta,ni-1.0); /* beta^n * zeta^n-1 */
+ b=(1+zeta*tmp); /* 1 + beta^n zeta^n */
+ db=chi*pow(b,-1.0/(2*ni)-1); /* x(...)^(-1/2n - 1) */
+ b=db*b; /* b_ij */
+ db*=-0.5*tmp; /* db_ij */
+ v3_scale(&force,&(exchange->dzeta_ij),f_a*db);
+ v3_scale(&temp,dist_ij,df_a*b);
+ v3_add(&force,&force,&temp);
+ v3_scale(&force,&force,f_c);
+ }
+ v3_scale(&temp,dist_ij,df_c*b*f_a);
+ v3_add(&force,&force,&temp);
+ v3_scale(&force,&force,-0.5);
+
+ /* 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);
+
+ /* dVji */
+ zeta=exchange->zeta_ji;
+ if(zeta==0.0) {
+ moldyn->debug++;
+ b=chi;
+ v3_scale(&force,dist_ij,df_a*b*f_c);
+ }
+ else {
+ tmp=betajnj*pow(zeta,nj-1.0); /* beta^n * zeta^n-1 */
+ b=(1+zeta*tmp); /* 1 + beta^n zeta^n */
+ db=chi*pow(b,-1.0/(2*nj)-1); /* x(...)^(-1/2n - 1) */
+ b=db*b; /* b_ij */
+ db*=-0.5*tmp; /* db_ij */
+ v3_scale(&force,&(exchange->dzeta_ji),f_a*db);
+ v3_scale(&temp,dist_ij,df_a*b);
+ v3_add(&force,&force,&temp);
+ v3_scale(&force,&force,f_c);
+ }
+ v3_scale(&temp,dist_ij,df_c*b*f_a);
+ v3_add(&force,&force,&temp);
+ v3_scale(&force,&force,-0.5);
+
+ /* add 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;
+}
+
+/* tersoff 3 body part */
+
+int tersoff_mult_3bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,t_atom *ak,u8 bc) {
+
+ t_tersoff_mult_params *params;
+ t_tersoff_exchange *exchange;
+ t_3dvec dist_ij,dist_ik,dist_jk;
+ t_3dvec temp1,temp2;
+ t_3dvec *dzeta;
+ double R,S,S2,s_r;
+ double B,mu;
+ 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 f_c_jk;
+ double n,c,d,h;
+ double c2,d2,c2d2;
+ double cos_theta,d_costheta1,d_costheta2;
+ double h_cos,d2_h_cos2;
+ double frac,g,zeta,chi;
+ double tmp;
+ int brand;
+
+ params=moldyn->pot3b_params;
+ exchange=&(params->exchange);
+
+ if(!(exchange->run3bp))
+ return 0;
+
+ /*
+ * calc of 3bp contribution of V_ij and dV_ij/ji/jk &
+ * 2bp contribution of dV_jk
+ *
+ * for Vij and dV_ij we still need:
+ * - b_ij, db_ij (zeta_ij)
+ * - f_c_ik, df_c_ik, constants_i, cos_theta_ijk, d_costheta_ijk
+ *
+ * for dV_ji we still need:
+ * - b_ji, db_ji (zeta_ji)
+ * - f_c_jk, d_c_jk, constants_j, cos_theta_jik, d_costheta_jik
+ *
+ * for dV_jk we need:
+ * - f_c_jk
+ * - f_a_jk
+ * - db_jk (zeta_jk)
+ * - f_c_ji, df_c_ji, constants_j, cos_theta_jki, d_costheta_jki
+ *
+ */
+
+ /*
+ * get exchange data
+ */
+
+ /* 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;
+ df_c=exchange->df_c;
+
+ /*
+ * calculate unknown values now ...
+ */
+
+ /* V_ij and dV_ij stuff (in b_ij there is f_c_ik) */
+
+ /* dist_ik, d_ik */
+ v3_sub(&dist_ik,&(ak->r),&(ai->r));
+ if(bc) check_per_bound(moldyn,&dist_ik);
+ d_ik2=v3_absolute_square(&dist_ik);
+
+ /* ik constants */
+ 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_ik2<S2) {
+
+ /* now we need d_ik */
+ d_ik=sqrt(d_ik2);
+
+ /* get constants_i from exchange data */
+ n=*(exchange->n_i);
+ c=*(exchange->c_i);
+ d=*(exchange->d_i);
+ h=*(exchange->h_i);
+ c2=exchange->ci2;
+ d2=exchange->di2;
+ c2d2=exchange->ci2di2;
+
+ /* cosine of theta_ijk by scalaproduct */
+ rr=v3_scalar_product(&dist_ij,&dist_ik);
+ dd=d_ij*d_ik;
+ cos_theta=rr/dd;
+
+ /* d_costheta */
+ tmp=1.0/dd;
+ d_costheta1=cos_theta/d_ij2-tmp;
+ d_costheta2=cos_theta/d_ik2-tmp;
+
+ /* some usefull values */
+ h_cos=(h-cos_theta);
+ d2_h_cos2=d2+(h_cos*h_cos);
+ frac=c2/(d2_h_cos2);
+
+ /* g(cos_theta) */
+ g=1.0+c2d2-frac;
+
+ /* d_costheta_ij and dg(cos_theta) - needed in any case! */
+ v3_scale(&temp1,&dist_ij,d_costheta1);
+ v3_scale(&temp2,&dist_ik,d_costheta2);
+ v3_add(&temp1,&temp1,&temp2);
+ v3_scale(&temp1,&temp1,-2.0*frac*h_cos/d2_h_cos2); /* dg */
+
+ /* f_c_ik & df_c_ik + {d,}zeta contribution */
+ dzeta=&(exchange->dzeta_ij);
+ if(d_ik<R) {
+ /* {d,}f_c_ik */
+ // => f_c_ik=1.0;
+ // => df_c_ik=0.0; of course we do not set this!
+
+ /* zeta_ij */
+ exchange->zeta_ij+=g;
+
+ /* dzeta_ij */
+ v3_add(dzeta,dzeta,&temp1);
+ }
+ else {
+ /* {d,}f_c_ik */
+ 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));
+
+ /* zeta_ij */
+ exchange->zeta_ij+=f_c_ik*g;
+
+ /* dzeta_ij */
+ v3_scale(&temp1,&temp1,f_c_ik);
+ v3_scale(&temp2,&dist_ik,g*df_c_ik);
+ v3_add(&temp1,&temp1,&temp2);
+ v3_add(dzeta,dzeta,&temp1);
}
+ }
- /* neighbours due to boundary conditions */
- for(j=c;j<27;j++) {
- this=&(neighbour[j]);
- list_reset(this); /* check boundary conditions */
- if(this->start!=NULL) {
+ /* dV_ji stuff (in b_ji there is f_c_jk) + dV_jk stuff! */
+
+ /* dist_jk, d_jk */
+ v3_sub(&dist_jk,&(ak->r),&(aj->r));
+ if(bc) check_per_bound(moldyn,&dist_jk);
+ d_jk2=v3_absolute_square(&dist_jk);
+
+ /* jk constants */
+ 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;
+ }
- do {
- printf("out bound: %d\n",j);
- btom=this->current->data;
- v3_sub(&distance,&(atom[i].r),&(btom->r));
- v3_per_bound(&distance,&(moldyn->dim));
- d=v3_absolute_square(&distance); /* r^2 */
- if(d<=moldyn->cutoff_square) {
- d=1.0/d; /* 1/r^2 */
- h1=d*d; /* 1/r^4 */
- h2*=d; /* 1/r^6 */
- h1=h2*h2; /* 1/r^12 */
- u+=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(&(atom[i].f),&(atom[i].f),
- &force);
- }
- } while(list_next(this)!=L_NO_NEXT_ELEMENT);
+ /* zeta_ji/dzeta_ji contribution only for d_jk < S_jk */
+ if(d_jk2<S2) {
+
+ /* now we need d_ik */
+ d_jk=sqrt(d_jk2);
+
+ /* constants_j from exchange data */
+ n=*(exchange->n_j);
+ c=*(exchange->c_j);
+ d=*(exchange->d_j);
+ h=*(exchange->h_j);
+ c2=exchange->cj2;
+ d2=exchange->dj2;
+ c2d2=exchange->cj2dj2;
+
+ /* cosine of theta_jik by scalaproduct */
+ 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/dd;
+ d_costheta2=cos_theta/d_ij2;
+
+ /* some usefull values */
+ h_cos=(h-cos_theta);
+ d2_h_cos2=d2+(h_cos*h_cos);
+ frac=c2/(d2_h_cos2);
+
+ /* g(cos_theta) */
+ g=1.0+c2d2-frac;
+
+ /* 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_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) {
+ /* f_c_jk */
+ f_c_jk=1.0;
+
+ /* zeta_ji */
+ exchange->zeta_ji+=g;
+
+ /* dzeta_ji */
+ v3_add(dzeta,dzeta,&temp1);
+ }
+ else {
+ /* f_c_jk */
+ s_r=S-R;
+ arg=M_PI*(d_jk-R)/s_r;
+ f_c_jk=0.5+0.5*cos(arg);
+
+ /* zeta_ji */
+ exchange->zeta_ji+=f_c_jk*g;
+
+ /* 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,&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 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(&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
+
}
- moldyn->energy=u;
-
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;
+}