#include "potentials/harmonic_oscillator.h"
#include "potentials/lennard_jones.h"
#include "potentials/albe.h"
+#include "potentials/albe_orig.h"
#ifdef TERSOFF_ORIG
#include "potentials/tersoff_orig.h"
#else
case STAGE_DISPLACE_ATOM:
psize=sizeof(t_displace_atom_params);
break;
+ case STAGE_DEL_ATOMS:
+ psize=sizeof(t_del_atoms_params);
+ break;
+ case STAGE_MODIFY_ATOMS:
+ psize=sizeof(t_modify_atoms_params);
+ break;
case STAGE_INSERT_ATOMS:
psize=sizeof(t_insert_atoms_params);
break;
+ case STAGE_INSERT_MIXED_ATOMS:
+ psize=sizeof(t_insert_mixed_atoms_params);
+ break;
case STAGE_CONTINUE:
psize=sizeof(t_continue_params);
break;
case STAGE_CHSATTR:
psize=sizeof(t_chsattr_params);
break;
+ case STAGE_SET_TEMP:
+ psize=sizeof(t_set_temp_params);
+ break;
+ case STAGE_SET_TIMESTEP:
+ psize=sizeof(t_set_timestep_params);
+ break;
+ case STAGE_FILL:
+ psize=sizeof(t_fill_params);
+ break;
+ case STAGE_THERMAL_INIT:
+ psize=0;
+ break;
+ case STAGE_CRT:
+ psize=sizeof(t_crt_params);
+ break;
default:
printf("%s unknown stage type: %02x\n",ME,type);
return -1;
char error[128];
char line[128];
char *wptr;
- char word[16][64];
+ char word[32][64];
int wcnt;
int i,o;
t_displace_atom_params dap;
+ t_modify_atoms_params map;
t_insert_atoms_params iap;
+ t_insert_mixed_atoms_params imp;
t_continue_params cp;
t_anneal_params ap;
t_chaattr_params cap;
t_chsattr_params csp;
+ t_set_temp_params stp;
+ t_set_timestep_params stsp;
+ t_fill_params fp;
+ t_del_atoms_params delp;
+ t_crt_params crtp;
/* open config file */
fd=open(mdrun->cfile,O_RDONLY);
// reset
memset(&iap,0,sizeof(t_insert_atoms_params));
+ memset(&map,0,sizeof(t_modify_atoms_params));
+ memset(&imp,0,sizeof(t_insert_mixed_atoms_params));
memset(&cp,0,sizeof(t_continue_params));
memset(&ap,0,sizeof(t_anneal_params));
memset(&cap,0,sizeof(t_chaattr_params));
memset(&csp,0,sizeof(t_chsattr_params));
+ memset(&stp,0,sizeof(t_set_temp_params));
+ memset(&stsp,0,sizeof(t_set_timestep_params));
+ memset(&fp,0,sizeof(t_fill_params));
+ memset(&delp,0,sizeof(t_del_atoms_params));
+ memset(&crtp,0,sizeof(t_crt_params));
// get command + args
wcnt=0;
if(!strncmp(word[0],"potential",9)) {
if(!strncmp(word[1],"albe",4))
mdrun->potential=MOLDYN_POTENTIAL_AM;
+ if(!strncmp(word[1],"albe_o",6))
+ mdrun->potential=MOLDYN_POTENTIAL_AO;
if(!strncmp(word[1],"tersoff",7))
mdrun->potential=MOLDYN_POTENTIAL_TM;
if(!strncmp(word[1],"ho",2))
mdrun->lattice=FCC;
if(!strncmp(word[1],"diamond",7))
mdrun->lattice=DIAMOND;
+ if(!strncmp(word[1],"none",4))
+ mdrun->lattice=NONE;
+ if(wcnt==3)
+ mdrun->lc=atof(word[2]);
}
else if(!strncmp(word[0],"element1",8)) {
mdrun->element1=atoi(word[1]);
- mdrun->m1=pse_mass[mdrun->element1];
}
else if(!strncmp(word[0],"element2",8)) {
mdrun->element2=atoi(word[1]);
- mdrun->m2=pse_mass[mdrun->element2];
}
else if(!strncmp(word[0],"fill",6)) {
- // only lc mode by now
- mdrun->lx=atoi(word[2]);
- mdrun->ly=atoi(word[3]);
- mdrun->lz=atoi(word[4]);
- mdrun->lc=atof(word[5]);
+ // default values
+ fp.fill_element=mdrun->element1;
+ fp.fill_brand=0;
+ fp.lattice=mdrun->lattice;
+ fp.p_params.type=0;
+ fp.d_params.type=0;
+ fp.d_params.stype=0;
+ // parse fill command
+ i=1;
+ while(i<wcnt) {
+ if(!strncmp(word[i],"lc",2)) {
+ fp.lx=atoi(word[++i]);
+ fp.ly=atoi(word[++i]);
+ fp.lz=atoi(word[++i]);
+ fp.lc=atof(word[++i]);
+ mdrun->lc=fp.lc;
+ continue;
+ }
+ if(!strncmp(word[i],"eb",2)) {
+ fp.fill_element=atoi(word[++i]);
+ fp.fill_brand=atoi(word[++i]);
+ continue;
+ }
+ if(word[i][0]=='p') {
+ i+=1;
+ switch(word[i][0]) {
+ case 'i':
+ if(word[i][1]=='r')
+ fp.p_params.type=PART_INSIDE_R;
+ else
+ fp.p_params.type=PART_INSIDE_D;
+ break;
+ case 'o':
+ if(word[i][1]=='r')
+ fp.p_params.type=PART_OUTSIDE_R;
+ else
+ fp.p_params.type=PART_OUTSIDE_D;
+ break;
+ default:
+ break;
+ }
+ if((fp.p_params.type==PART_INSIDE_R)||
+ (fp.p_params.type==PART_OUTSIDE_R)) {
+ fp.p_params.r=atof(word[++i]);
+ fp.p_params.p.x=atof(word[++i]);
+ fp.p_params.p.y=atof(word[++i]);
+ fp.p_params.p.z=atof(word[++i]);
+ }
+ if((fp.p_params.type==PART_INSIDE_D)||
+ (fp.p_params.type==PART_OUTSIDE_D)) {
+ fp.p_params.p.x=atof(word[++i]);
+ fp.p_params.p.y=atof(word[++i]);
+ fp.p_params.p.z=atof(word[++i]);
+ fp.p_params.d.x=atof(word[++i]);
+ fp.p_params.d.y=atof(word[++i]);
+ fp.p_params.d.z=atof(word[++i]);
+ }
+ continue;
+ }
+ if(word[i][0]=='d') {
+ switch(word[++i][0]) {
+ case '0':
+
+ fp.d_params.type=DEFECT_TYPE_0D;
+ if(!strncmp(word[i+1],"dbx",3)) {
+ fp.d_params.stype=DEFECT_STYPE_DB_X;
+ }
+ if(!strncmp(word[i+1],"dby",3)) {
+ fp.d_params.stype=DEFECT_STYPE_DB_Y;
+ }
+ if(!strncmp(word[i+1],"dbz",3)) {
+ fp.d_params.stype=DEFECT_STYPE_DB_Z;
+ }
+ if(!strncmp(word[i+1],"dbr",3)) {
+ fp.d_params.stype=DEFECT_STYPE_DB_R;
+ }
+ i+=1;
+ fp.d_params.od=atof(word[++i]);
+ fp.d_params.dd=atof(word[++i]);
+ fp.d_params.element=atoi(word[++i]);
+ fp.d_params.brand=atoi(word[++i]);
+ // parsed in future
+ fp.d_params.attr=ATOM_ATTR_HB|ATOM_ATTR_VA;
+ fp.d_params.attr|=ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP;
+ break;
+
+ case '1':
+ fp.d_params.type=DEFECT_TYPE_1D;
+ break;
+ case '2':
+ fp.d_params.type=DEFECT_TYPE_2D;
+ break;
+ case '3':
+ fp.d_params.type=DEFECT_TYPE_3D;
+ break;
+ default:
+ break;
+ }
+ continue;
+
+ }
+ // offset
+ if(word[i][0]=='o') {
+ fp.o_params.o.x=atof(word[++i])*fp.lc;
+ fp.o_params.o.y=atof(word[++i])*fp.lc;
+ fp.o_params.o.z=atof(word[++i])*fp.lc;
+ fp.o_params.use=1;
+ continue;
+ }
+ i+=1;
+ }
+ add_stage(mdrun,STAGE_FILL,&fp);
+ }
+ else if(!strncmp(word[0],"thermal_init",12)) {
+ add_stage(mdrun,STAGE_THERMAL_INIT,NULL);
}
else if(!strncmp(word[0],"aattr",5)) {
// for aatrib line we need a special stage
case 'e':
cap.type|=CHAATTR_ELEMENT;
break;
+ case 'n':
+ cap.type|=CHAATTR_NUMBER;
default:
break;
}
}
i=2;
if(cap.type&CHAATTR_REGION) {
- cap.x0=atof(word[1]);
- cap.y0=atof(word[2]);
- cap.z0=atof(word[3]);
- cap.x1=atof(word[4]);
- cap.y1=atof(word[5]);
- cap.z1=atof(word[6]);
+ cap.x0=atof(word[2]);
+ cap.y0=atof(word[3]);
+ cap.z0=atof(word[4]);
+ cap.x1=atof(word[5]);
+ cap.y1=atof(word[6]);
+ cap.z1=atof(word[7]);
i+=6;
}
if(cap.type&CHAATTR_ELEMENT) {
cap.element=atoi(word[i]);
i+=1;
}
+ if(cap.type&CHAATTR_NUMBER) {
+ cap.element=atoi(word[i]);
+ i+=1;
+ }
for(o=0;o<strlen(word[i]);o++) {
switch(word[i][o]) {
case 'b':
csp.type=0;
for(i=1;i<wcnt;i++) {
if(!strncmp(word[i],"pctrl",5)) {
- csp.ptau=0.01/(atof(word[++i])*GPA);
+ csp.ptau=atof(word[++i]);
+ if(csp.ptau>0)
+ csp.ptau=0.01/(csp.ptau*GPA);
csp.type|=CHSATTR_PCTRL;
}
if(!strncmp(word[i],"tctrl",5)) {
dap.dz=atof(word[5]);
add_stage(mdrun,STAGE_DISPLACE_ATOM,&dap);
}
+ else if(!strncmp(word[1],"del_atoms",9)) {
+ delp.o.x=atof(word[2]);
+ delp.o.y=atof(word[3]);
+ delp.o.z=atof(word[4]);
+ delp.r=atof(word[5]);
+ add_stage(mdrun,STAGE_DEL_ATOMS,&delp);
+ }
+ else if(!strncmp(word[1],"mod_atoms",8)) {
+ i=2;
+ while(i<wcnt) {
+ if(!strncmp(word[i],"t",1)) {
+ map.tag=atoi(word[++i]);
+ i+=1;
+ }
+ if(!strncmp(word[i],"ekin",5)) {
+ map.ekin.x=atof(word[++i])*EV;
+ map.ekin.y=atof(word[++i])*EV;
+ map.ekin.z=atof(word[++i])*EV;
+ i+=1;
+ }
+ }
+ add_stage(mdrun,STAGE_MODIFY_ATOMS,&map);
+ }
else if(!strncmp(word[1],"ins_atoms",9)) {
iap.ins_steps=atoi(word[2]);
iap.ins_atoms=atoi(word[3]);
iap.y0=atof(word[9]);
iap.z0=atof(word[10]);
break;
+ case 'P':
+ iap.type=INS_RELPOS;
+ iap.x0=atof(word[8]);
+ iap.y0=atof(word[9]);
+ iap.z0=atof(word[10]);
+ break;
case 'r':
- if(word[8][0]=='t') {
+ switch(word[8][0]) {
+
+ case 't':
iap.type=INS_TOTAL;
iap.cr=atof(word[9]);
- }
- else {
- iap.type=INS_REGION;
- iap.x0=atof(word[8]);
- iap.y0=atof(word[9]);
- iap.z0=atof(word[10]);
- iap.x1=atof(word[11]);
- iap.y1=atof(word[12]);
- iap.z1=atof(word[13]);
- iap.cr=atof(word[14]);
+ break;
+ case 'r':
+ iap.type=INS_RECT;
+ iap.x0=atof(word[9]);
+ iap.y0=atof(word[10]);
+ iap.z0=atof(word[11]);
+ iap.x1=atof(word[12]);
+ iap.y1=atof(word[13]);
+ iap.z1=atof(word[14]);
+ iap.cr=atof(word[15]);
+ break;
+ case 's':
+ iap.type=INS_SPHERE;
+ iap.x0=atof(word[9]);
+ iap.y0=atof(word[10]);
+ iap.z0=atof(word[11]);
+ iap.x1=atof(word[12]);
+ iap.cr=atof(word[13]);
+ break;
+ default:
+ break;
}
default:
break;
}
add_stage(mdrun,STAGE_INSERT_ATOMS,&iap);
}
+
+
+ // HERE WE GO ...
+
+ else if(!strncmp(word[1],"ins_m_atoms",11)) {
+ imp.element1=atoi(word[2]);
+ imp.element2=atoi(word[3]);
+ imp.amount1=atoi(word[4]);
+ imp.amount2=atoi(word[5]);
+ imp.brand1=atoi(word[6]);
+ imp.brand2=atoi(word[7]);
+ imp.crmin=atof(word[8]);
+ imp.crmax=atof(word[9]);
+ /* do this later ...
+ for(i=0;i<strlen(word[8]);i++) {
+ switch(word[8][i]) {
+ case 'b':
+ imp.attr|=ATOM_ATTR_VB;
+ break;
+ case 'h':
+ imp.attr|=ATOM_ATTR_HB;
+ break;
+ case 'v':
+ imp.attr|=ATOM_ATTR_VA;
+ break;
+ case 'f':
+ imp.attr|=ATOM_ATTR_FP;
+ break;
+ case '1':
+ imp.attr|=ATOM_ATTR_1BP;
+ break;
+ case '2':
+ imp.attr|=ATOM_ATTR_2BP;
+ break;
+ case '3':
+ imp.attr|=ATOM_ATTR_3BP;
+ break;
+ default:
+ break;
+ }
+ }
+ */
+ imp.attr1=ATOM_ATTR_HB|ATOM_ATTR_VA|ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_FP;
+ imp.attr2=ATOM_ATTR_HB|ATOM_ATTR_VA|ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_FP;
+ add_stage(mdrun,STAGE_INSERT_MIXED_ATOMS,&imp);
+ }
+
+
+
+
+
else if(!strncmp(word[1],"continue",8)) {
cp.runs=atoi(word[2]);
add_stage(mdrun,STAGE_CONTINUE,&cp);
ap.count=0;
ap.runs=atoi(word[2]);
ap.dt=atof(word[3]);
+ ap.interval=atoi(word[4]);
add_stage(mdrun,STAGE_ANNEAL,&ap);
}
+ else if(!strncmp(word[1],"set_temp",8)) {
+ if(word[2][0]=='c') {
+ stp.type=SET_TEMP_CURRENT;
+ stp.val=0.0;
+ }
+ else {
+ stp.type=SET_TEMP_VALUE;
+ stp.val=atof(word[2]);
+ }
+ add_stage(mdrun,STAGE_SET_TEMP,&stp);
+ }
+ else if(!strncmp(word[1],"set_timestep",12)) {
+ stsp.tau=atof(word[2]);
+ add_stage(mdrun,STAGE_SET_TIMESTEP,&stsp);
+ }
+ else if(!strncmp(word[1],"crt",3)) {
+ crtp.type=atoi(word[2]);
+ crtp.steps=atoi(word[3]);
+ strncpy(crtp.file,word[4],127);
+ add_stage(mdrun,STAGE_CRT,&crtp);
+ }
else {
printf("%s unknown stage type: %s\n",
ME,word[1]);
return 0;
}
+ int del_atoms(t_moldyn *moldyn,t_mdrun *mdrun) {
+
+ t_stage *stage;
+ t_del_atoms_params *delp;
+ int i;
+ t_3dvec dist;
+ u8 outer;
+
+ outer=0;
+ stage=mdrun->stage.current->data;
+ delp=stage->params;
+
+ if(delp->r<0)
+ outer=1;
+
+ for(i=0;i<moldyn->count;i++) {
+ v3_sub(&dist,&(delp->o),&(moldyn->atom[i].r));
+ //printf("%d ----> %f %f %f = %f | %f\n",i,dist.x,dist.y,dist.z,v3_absolute_square(&dist),delp->r*delp->r);
+ if(v3_absolute_square(&dist)<=(delp->r*delp->r)) {
+ if(!outer) {
+ del_atom(moldyn,moldyn->atom[i].tag);
+ printf("%s atom deleted: %d %d %d\n",ME,
+ moldyn->atom[i].tag,
+ moldyn->atom[i].element,
+ moldyn->atom[i].brand);
+ }
+ }
+ else {
+ if(outer) {
+ del_atom(moldyn,moldyn->atom[i].tag);
+ printf("%s atom deleted: %d %d %d\n",ME,
+ moldyn->atom[i].tag,
+ moldyn->atom[i].element,
+ moldyn->atom[i].brand);
+ }
+ }
+ }
+
+ return 0;
+ }
+
+ int modify_atoms(t_moldyn *moldyn,t_mdrun *mdrun) {
+
+ t_modify_atoms_params *map;
+ t_stage *stage;
+ t_atom *atom;
+ t_3dvec v;
+ int i;
+
+ atom=moldyn->atom;
+ stage=mdrun->stage.current->data;
+ map=stage->params;
+ v.x=0.0; v.y=0.0; v.z=0.0;
+
+ for(i=0;i<moldyn->count;i++) {
+ if(atom[i].tag==map->tag) {
+ v.x=sqrt(2.0*fabs(map->ekin.x)/atom[i].mass);
+ if(map->ekin.x<0.0)
+ v.x=-v.x;
+ v.y=sqrt(2.0*fabs(map->ekin.y)/atom[i].mass);
+ if(map->ekin.y<0.0)
+ v.y=-v.y;
+ v.z=sqrt(2.0*fabs(map->ekin.z)/atom[i].mass);
+ if(map->ekin.z<0.0)
+ v.z=-v.z;
+ v3_copy(&(atom[i].v),&v);
+ printf("%s atom modified: v = (%f %f %f)\n",
+ ME,v.x,v.y,v.z);
+ }
+ }
+
+ return 0;
+ }
+
int insert_atoms(t_moldyn *moldyn,t_mdrun *mdrun) {
t_insert_atoms_params *iap;
z0=-z/2.0;
cr_check=TRUE;
break;
- case INS_REGION:
+ case INS_RECT:
x=iap->x1-iap->x0;
x0=iap->x0;
y=iap->y1-iap->y0;
z0=iap->z0;
cr_check=TRUE;
break;
+ case INS_SPHERE:
+ x=2.0*iap->x1;
+ x0=iap->x0-iap->x1;
+ y=x;
+ y0=iap->y0-iap->x1;
+ z=x;
+ z0=iap->z0-iap->x1;
+ cr_check=TRUE;
+ break;
case INS_POS:
+ case INS_RELPOS:
x0=iap->x0;
y0=iap->y0;
z0=iap->z0;
while(cnt<iap->ins_atoms) {
run=1;
while(run) {
- if(iap->type!=INS_POS) {
+ if((iap->type!=INS_POS)&&(iap->type!=INS_RELPOS)) {
r.x=rand_get_double(&(moldyn->random))*x;
r.y=rand_get_double(&(moldyn->random))*y;
r.z=rand_get_double(&(moldyn->random))*z;
r.y=0.0;
r.z=0.0;
}
- r.x+=x0;
- r.y+=y0;
- r.z+=z0;
+ if(iap->type==INS_RELPOS) {
+ r.x+=x0*mdrun->lc;
+ r.y+=y0*mdrun->lc;
+ r.z+=z0*mdrun->lc;
+ }
+ else {
+ r.x+=x0;
+ r.y+=y0;
+ r.z+=z0;
+ }
// offset
if(iap->type!=INS_TOTAL) {
r.x+=o;
dmin=d;
}
}
+ if(iap->type==INS_SPHERE) {
+ if((r.x-iap->x0)*(r.x-iap->x0)+
+ (r.y-iap->y0)*(r.y-iap->y0)+
+ (r.z-iap->z0)*(r.z-iap->z0)>
+ (iap->x1*iap->x1)) {
+ run=1;
+ }
+ }
}
- add_atom(moldyn,iap->element,pse_mass[iap->element],
+ add_atom(moldyn,iap->element,
iap->brand,iap->attr,&r,&v);
printf("%s atom inserted (%d/%d): %f %f %f\n",
ME,(iap->cnt_steps+1)*iap->ins_atoms,
iap->ins_steps*iap->ins_atoms,r.x,r.y,r.z);
- printf(" -> d2 = %f/%f\n",dmin,iap->cr*iap->cr);
+ printf(" attributes: ");
+ if(iap->attr&ATOM_ATTR_VB)
+ printf("b ");
+ if(iap->attr&ATOM_ATTR_HB)
+ printf("h ");
+ if(iap->attr&ATOM_ATTR_VA)
+ printf("v ");
+ if(iap->attr&ATOM_ATTR_FP)
+ printf("f ");
+ if(iap->attr&ATOM_ATTR_1BP)
+ printf("1 ");
+ if(iap->attr&ATOM_ATTR_2BP)
+ printf("2 ");
+ if(iap->attr&ATOM_ATTR_3BP)
+ printf("3 ");
+ printf("\n");
+ printf(" d2 = %f/%f\n",dmin,iap->cr*iap->cr);
cnt+=1;
}
return 0;
}
+ int insert_mixed_atoms(t_moldyn *moldyn,t_mdrun *mdrun) {
+
+ t_stage *stage;
+ t_insert_mixed_atoms_params *imp;
+ t_atom *atom;
+ double x,x0,y,y0,z,z0;
+ double dmin,d,cmin,cmax;
+ u8 retry;
+ t_3dvec r,v,dist;
+ int i;
+
+
+ stage=mdrun->stage.current->data;
+ imp=stage->params;
+
+ x=moldyn->dim.x;
+ x0=-x/2.0;
+ y=moldyn->dim.y;
+ y0=-y/2.0;
+ z=moldyn->dim.z;
+ z0=-z/2.0;
+
+ v.x=0.0;
+ v.y=0.0;
+ v.z=0.0;
+
+ cmin=imp->crmin*imp->crmin;
+ cmax=imp->crmax*imp->crmax;
+
+ while(imp->amount1|imp->amount2) {
+ if(imp->amount1) {
+ retry=1;
+ while(retry) {
+ retry=0;
+ r.x=rand_get_double(&(moldyn->random))*x;
+ r.y=rand_get_double(&(moldyn->random))*y;
+ r.z=rand_get_double(&(moldyn->random))*z;
+ r.x+=x0;
+ r.y+=y0;
+ r.z+=z0;
+ dmin=1000.0; // for sure too high!
+ for(i=0;i<moldyn->count;i++) {
+ atom=&(moldyn->atom[i]);
+ v3_sub(&dist,&(atom->r),&r);
+ check_per_bound(moldyn,&dist);
+ d=v3_absolute_square(&dist);
+ if(d<cmin) {
+ retry=1;
+ break;
+ }
+ if(d<dmin)
+ dmin=d;
+ }
+ if(dmin!=1000.0)
+ if(dmin>cmax)
+ retry=1;
+ }
+ add_atom(moldyn,imp->element1,
+ imp->brand1,imp->attr1,&r,&v);
+ printf("%s (mixed) atom inserted (%d): %f %f %f\n",
+ ME,imp->amount1,r.x,r.y,r.z);
+ printf(" -> d2 = %f/%f/%f\n",dmin,cmin,cmax);
+ imp->amount1-=1;
+ }
+ if(imp->amount2) {
+ retry=1;
+ while(retry) {
+ retry=0;
+ r.x=rand_get_double(&(moldyn->random))*x;
+ r.y=rand_get_double(&(moldyn->random))*y;
+ r.z=rand_get_double(&(moldyn->random))*z;
+ r.x+=x0;
+ r.y+=y0;
+ r.z+=z0;
+ dmin=1000.0; // for sure too high!
+ for(i=0;i<moldyn->count;i++) {
+ atom=&(moldyn->atom[i]);
+ v3_sub(&dist,&(atom->r),&r);
+ check_per_bound(moldyn,&dist);
+ d=v3_absolute_square(&dist);
+ if(d<cmin) {
+ retry=1;
+ break;
+ }
+ if(d<dmin)
+ dmin=d;
+ }
+ if(dmin!=1000.0)
+ if(dmin>cmax)
+ retry=1;
+ }
+ add_atom(moldyn,imp->element2,
+ imp->brand2,imp->attr2,&r,&v);
+ printf("%s (mixed) atom inserted (%d): %f %f %f\n",
+ ME,imp->amount2,r.x,r.y,r.z);
+ printf(" -> d2 = %f/%f/%f\n",dmin,cmin,cmax);
+ imp->amount2-=1;
+ }
+ }
+
+ return 0;
+ }
+
int chaatr(t_moldyn *moldyn,t_mdrun *mdrun) {
t_stage *stage;
if(cap->element!=atom->element)
continue;
}
+ if(cap->type&CHAATTR_NUMBER) {
+ if(cap->element!=atom->tag)
+ continue;
+ }
if(cap->type&CHAATTR_REGION) {
- if(cap->x0<atom->r.x)
+ if(cap->x0>atom->r.x)
continue;
- if(cap->y0<atom->r.y)
+ if(cap->y0>atom->r.y)
continue;
- if(cap->z0<atom->r.z)
+ if(cap->z0>atom->r.z)
continue;
- if(cap->x1>atom->r.x)
+ if(cap->x1<atom->r.x)
continue;
- if(cap->y1>atom->r.y)
+ if(cap->y1<atom->r.y)
continue;
- if(cap->z1>atom->r.z)
+ if(cap->z1<atom->r.z)
continue;
}
+ if(!(cap->type&CHAATTR_TOTALV))
+ printf(" changing attributes of atom %d (0x%x)\n",
+ i,cap->attr);
atom->attr=cap->attr;
}
+ printf("\n\n");
+
return 0;
}
if(csp->ptau>0)
set_p_scale(moldyn,P_SCALE_BERENDSEN,csp->ptau);
else
- set_p_scale(moldyn,P_SCALE_BERENDSEN,csp->ptau);
+ set_p_scale(moldyn,P_SCALE_NONE,1.0);
}
if(csp->type&CHSATTR_TCTRL) {
if(csp->ttau>0)
set_t_scale(moldyn,T_SCALE_BERENDSEN,csp->ttau);
else
- set_t_scale(moldyn,T_SCALE_BERENDSEN,csp->ttau);
+ set_t_scale(moldyn,T_SCALE_NONE,1.0);
}
if(csp->type&CHSATTR_PRELAX) {
if(csp->dp<0)
return 0;
}
+ int crt(t_moldyn *moldyn,t_mdrun *mdrun) {
+
+ t_stage *stage;
+ t_crt_params *crtp;
+
+ int fd;
+ char line[128];
+ char *wptr;
+ int acount;
+ int ret;
+ void *ptr;
+
+ t_atom *atom;
+ t_3dvec disp;
+ double frac;
+ int i;
+
+ stage=mdrun->stage.current->data;
+ crtp=stage->params;
+
+ acount=0;
+
+ /* initial stuff */
+
+ if(crtp->count==0) {
+ printf(" crt init\n");
+ // read final positions, constraints and do the alloc
+ fd=open(crtp->file,O_RDONLY);
+ if(fd<0) {
+ perror("[mdrun] FATAL reading constraints file");
+ return fd;
+ }
+ while(1) {
+ ret=get_line(fd,line,128);
+ // check for end of file
+ if(ret<=0) {
+ printf(" read %d atom positions\n",acount);
+ if(acount!=moldyn->count)
+ printf(" atom count mismatch!!!\n");
+ printf("\n");
+ break;
+ }
+ // ignore # lines and \n
+ if((line[0]=='#')|(ret==1))
+ continue;
+ // allocate new memory
+ ptr=realloc(crtp->r_fin,(acount+1)*sizeof(t_3dvec));
+ if(ptr==NULL) {
+ perror("[mdrun] FATAL realloc crt positions");
+ return -1;
+ }
+ crtp->r_fin=ptr;
+ ptr=realloc(constraints,(acount+1)*3*sizeof(u8));
+ if(ptr==NULL) {
+ perror("[mdrun] FATAL realloc crt constraints");
+ return -1;
+ }
+ constraints=ptr;
+ // ignore type
+ wptr=strtok(line," \t");
+ // read x y z
+ wptr=strtok(NULL," \t");
+ crtp->r_fin[acount].x=atof(wptr);
+ wptr=strtok(NULL," \t");
+ crtp->r_fin[acount].y=atof(wptr);
+ wptr=strtok(NULL," \t");
+ crtp->r_fin[acount].z=atof(wptr);
+ // read constraints
+ wptr=strtok(NULL," \t");
+ constraints[3*acount]=atoi(wptr);
+ wptr=strtok(NULL," \t");
+ constraints[3*acount+1]=atoi(wptr);
+ wptr=strtok(NULL," \t");
+ constraints[3*acount+2]=atoi(wptr);
+ // done reading
+ acount+=1;
+ }
+ close(fd);
+ // allocate trafo angles
+ trafo_angle=malloc(acount*2*sizeof(double));
+ if(trafo_angle==NULL) {
+ perror("[mdrun] FATAL alloc trafo angles");
+ return -1;
+ }
+ // set crt mode
+ crtt=crtp->type;
+ }
+
+ /* write a save file s-crt_xofy.save */
+ snprintf(line,128,"%s/s-crt_%03dof%03d.save",
+ moldyn->vlsdir,crtp->count,crtp->steps);
+ fd=open(line,O_WRONLY|O_TRUNC|O_CREAT,S_IRUSR|S_IWUSR);
+ if(fd<0) perror("[mdrun] crt save fd open");
+ else {
+ write(fd,moldyn,sizeof(t_moldyn));
+ write(fd,moldyn->atom,
+ moldyn->count*sizeof(t_atom));
+ }
+ close(fd);
+ /* visualize atoms */
+ visual_atoms(moldyn);
+
+ /* output energy */
+ printf(" crt energy: %d - %f\n\n",
+ crtp->count,(moldyn->ekin+moldyn->energy)/EV);
+
+ /* crt routines: calculate displacement + set individual constraints */
+
+ printf(" crt step %d of %d in total\n\n",crtp->count+1,crtp->steps);
+
+ if((crtp->type==1)|(crtp->count==0))
+ printf(" crt angle update\n\n");
+
+ for(i=0;i<moldyn->count;i++) {
+ // calc displacements
+ atom=moldyn->atom;
+ v3_sub(&disp,&(crtp->r_fin[i]),&(atom[i].r));
+ // angles
+ if((crtp->type==1)|(crtp->count==0)) {
+ trafo_angle[2*i]=atan2(disp.x,disp.y);
+ trafo_angle[2*i+1]=-atan2(disp.z,
+ sqrt(disp.x*disp.x+disp.y*disp.y));
+ }
+ // move atoms
+ frac=1.0/(crtp->steps-crtp->count);
+ v3_scale(&disp,&disp,frac);
+ v3_add(&(atom[i].r),&(atom[i].r),&disp);
+ }
+
+ return 0;
+ }
+
#define stage_print(m) if(!(stage->executed)) \
printf("%s",m)
t_stage *stage;
t_list *sl;
int steps;
- double tau;
u8 change_stage;
+ t_3dvec o;
t_insert_atoms_params *iap;
+ t_insert_mixed_atoms_params *imp;
t_continue_params *cp;
t_anneal_params *ap;
+ t_set_temp_params *stp;
+ t_set_timestep_params *stsp;
+ t_fill_params *fp;
+ t_crt_params *crtp;
moldyn=ptr1;
mdrun=ptr2;
/* get stage description */
stage=sl->current->data;
- /* default steps and tau values */
+ /* steps in next schedule */
steps=mdrun->relax_steps;
- tau=mdrun->timestep;
/* check whether relaxation steps are necessary */
if((check_pressure(moldyn,mdrun)==TRUE)&\
displace_atom(moldyn,mdrun);
change_stage=TRUE;
break;
+ case STAGE_DEL_ATOMS:
+ stage_print(" -> del atoms\n\n");
+ del_atoms(moldyn,mdrun);
+ change_stage=TRUE;
+ break;
+ case STAGE_MODIFY_ATOMS:
+ stage_print(" -> modify atoms\n\n");
+ modify_atoms(moldyn,mdrun);
+ change_stage=TRUE;
+ break;
case STAGE_INSERT_ATOMS:
stage_print(" -> insert atoms\n\n");
iap=stage->params;
insert_atoms(moldyn,mdrun);
iap->cnt_steps+=1;
break;
+
+
+
+ case STAGE_INSERT_MIXED_ATOMS:
+ stage_print(" -> insert mixed atoms\n\n");
+ imp=stage->params;
+ insert_mixed_atoms(moldyn,mdrun);
+ change_stage=TRUE;
+ break;
+
+
+
case STAGE_CONTINUE:
stage_print(" -> continue\n\n");
if(stage->executed==TRUE) {
set_temperature(moldyn,
moldyn->t_ref+ap->dt);
ap->count+=1;
+ steps=ap->interval;
break;
case STAGE_CHAATTR:
- stage_print(" -> chaattr\n\n");
+ stage_print(" -> change atom attributes\n\n");
chaatr(moldyn,mdrun);
change_stage=TRUE;
break;
case STAGE_CHSATTR:
- stage_print(" -> chsattr\n\n");
+ stage_print(" -> change sys attributes\n\n");
chsattr(moldyn,mdrun);
change_stage=TRUE;
break;
+ case STAGE_SET_TEMP:
+ stage_print(" -> set temperature\n\n");
+ stp=stage->params;
+ if(stp->type&SET_TEMP_CURRENT) {
+ set_temperature(moldyn,moldyn->t_avg);
+ }
+ else {
+ set_temperature(moldyn,stp->val);
+ }
+ change_stage=TRUE;
+ break;
+ case STAGE_SET_TIMESTEP:
+ stage_print(" -> set timestep\n\n");
+ stsp=stage->params;
+ mdrun->timestep=stsp->tau;
+ change_stage=TRUE;
+ break;
+ case STAGE_FILL:
+ stage_print(" -> fill lattice\n\n");
+ fp=stage->params;
+ switch(fp->lattice) {
+ case ZINCBLENDE:
+
+ o.x=0.5*0.25*fp->lc;
+ o.y=o.x;
+ o.z=o.x;
+ create_lattice(moldyn,
+ FCC,fp->lc,
+ mdrun->element1,
+ DEFAULT_ATOM_ATTR,0,
+ fp->lx,fp->ly,fp->lz,
+ &o,
+ &(fp->p_params),
+ &(fp->d_params),
+ &(fp->o_params));
+ o.x+=0.25*fp->lc;
+ o.y=o.x;
+ o.z=o.x;
+ create_lattice(moldyn,
+ FCC,fp->lc,
+ mdrun->element2,
+ DEFAULT_ATOM_ATTR,1,
+ fp->lx,fp->ly,fp->lz,
+ &o,
+ &(fp->p_params),
+ &(fp->d_params),
+ &(fp->o_params));
+ break;
+
+ default:
+
+ create_lattice(moldyn,
+ fp->lattice,fp->lc,
+ fp->fill_element,
+ DEFAULT_ATOM_ATTR,
+ fp->fill_brand,
+ fp->lx,fp->ly,fp->lz,
+ NULL,
+ &(fp->p_params),
+ &(fp->d_params),
+ &(fp->o_params));
+ break;
+ }
+ moldyn_bc_check(moldyn);
+ change_stage=TRUE;
+ break;
+ case STAGE_THERMAL_INIT:
+ stage_print(" -> thermal init\n\n");
+ thermal_init(moldyn,TRUE);
+ change_stage=TRUE;
+ break;
+ case STAGE_CRT:
+ stage_print(" -> constraint relaxation");
+ stage_print(" technique\n\n");
+ crtp=stage->params;
+ if(crtp->count==crtp->steps) {
+ free(constraints);
+ free(trafo_angle);
+ free(crtp->r_fin);
+ change_stage=TRUE;
+ break;
+ }
+ crt(moldyn,mdrun);
+ crtp->count+=1;
+ break;
default:
printf("%s unknwon stage type\n",ME);
break;
return 0;
}
steps=0;
- tau=mdrun->timestep;
}
}
}
/* continue simulation */
- moldyn_add_schedule(moldyn,steps,tau);
+ moldyn_add_schedule(moldyn,steps,mdrun->timestep);
return 0;
}
t_mdrun mdrun;
t_moldyn moldyn;
- t_3dvec o;
+ //t_3dvec o;
/* clear structs */
memset(&mdrun,0,sizeof(t_mdrun));
memset(&moldyn,0,sizeof(t_moldyn));
+ /* init crt variables */
+ crtt=0;
+ constraints=NULL;
+ trafo_angle=NULL;
+
/* parse arguments */
if(mdrun_parse_argv(&mdrun,argc,argv)<0)
return -1;
mdrun.element1,
mdrun.element2);
break;
+ case MOLDYN_POTENTIAL_AO:
+ albe_orig_mult_set_params(&moldyn,
+ mdrun.element1,
+ mdrun.element2);
+ break;
case MOLDYN_POTENTIAL_TM:
tersoff_mult_set_params(&moldyn,
mdrun.element1,
/* initial lattice and dimensions */
set_dim(&moldyn,mdrun.dim.x,mdrun.dim.y,mdrun.dim.z,mdrun.vis);
set_pbc(&moldyn,mdrun.pbcx,mdrun.pbcy,mdrun.pbcz);
+ /* replaced by fill stage !!
switch(mdrun.lattice) {
case FCC:
- create_lattice(&moldyn,FCC,mdrun.lc,mdrun.element1,
- mdrun.m1,DEFAULT_ATOM_ATTR,0,mdrun.lx,
- mdrun.ly,mdrun.lz,NULL);
+ create_lattice(&moldyn,FCC,mdrun.lc,mdrun.fill_element,
+ mdrun.m1,DEFAULT_ATOM_ATTR,
+ mdrun.fill_brand,mdrun.lx,
+ mdrun.ly,mdrun.lz,NULL,0,NULL);
break;
case DIAMOND:
- create_lattice(&moldyn,DIAMOND,mdrun.lc,mdrun.element1,
- mdrun.m1,DEFAULT_ATOM_ATTR,0,mdrun.lx,
- mdrun.ly,mdrun.lz,NULL);
+ create_lattice(&moldyn,DIAMOND,mdrun.lc,
+ mdrun.fill_element,
+ mdrun.m1,DEFAULT_ATOM_ATTR,
+ mdrun.fill_brand,mdrun.lx,
+ mdrun.ly,mdrun.lz,NULL,0,NULL);
break;
case ZINCBLENDE:
o.x=0.5*0.25*mdrun.lc; o.y=o.x; o.z=o.x;
create_lattice(&moldyn,FCC,mdrun.lc,mdrun.element1,
mdrun.m1,DEFAULT_ATOM_ATTR,0,mdrun.lx,
- mdrun.ly,mdrun.lz,&o);
+ mdrun.ly,mdrun.lz,&o,0,NULL);
o.x+=0.25*mdrun.lc; o.y=o.x; o.z=o.x;
create_lattice(&moldyn,FCC,mdrun.lc,mdrun.element2,
mdrun.m2,DEFAULT_ATOM_ATTR,1,mdrun.lx,
- mdrun.ly,mdrun.lz,&o);
+ mdrun.ly,mdrun.lz,&o,0,NULL);
+ break;
+ case NONE:
+ set_nn_dist(&moldyn,mdrun.nnd);
break;
default:
printf("%s unknown lattice type: %02x\n",
return -1;
}
moldyn_bc_check(&moldyn);
+ replaced by fill stage !! */
/* temperature and pressure */
set_temperature(&moldyn,mdrun.temperature);
set_pressure(&moldyn,mdrun.pressure);
+ /* replaced thermal_init stage
thermal_init(&moldyn,TRUE);
+ */
addsched:
/* first schedule */
#include <time.h>
#include <math.h>
+ #include <fpu_control.h>
+
+ #ifdef PARALLEL
+ #include <omp.h>
+ #endif
+
+ #if defined PTHREADS || defined VISUAL_THREAD
+ #include <pthread.h>
+ #endif
+
#include "moldyn.h"
#include "report/report.h"
#include "potentials/harmonic_oscillator.h"
#include "potentials/lennard_jones.h"
#include "potentials/albe.h"
+#include "potentials/albe_orig.h"
#ifdef TERSOFF_ORIG
#include "potentials/tersoff_orig.h"
#else
#include "potentials/tersoff.h"
#endif
+ /* pse */
+ #define PSE_MASS
+ #define PSE_NAME
+ #define PSE_COL
+ #include "pse.h"
+ #undef PSE_MASS
+ #undef PSE_NAME
+ #undef PSE_COL
+
+ #ifdef PTHREADS
+ /* global mutexes */
+ pthread_mutex_t *amutex;
+ pthread_mutex_t emutex;
+ #endif
+
+ /* fully constrained relaxation technique - global pointers */
+ u8 crtt;
+ u8 *constraints;
+ double *trafo_angle;
+
/*
* the moldyn functions
*/
printf("[moldyn] init\n");
+ /* only needed if compiled without -msse2 (float-store prob!) */
+ //fpu_set_rtd();
+
memset(moldyn,0,sizeof(t_moldyn));
moldyn->argc=argc;
rand_init(&(moldyn->random),NULL,1);
moldyn->random.status|=RAND_STAT_VERBOSE;
+ #ifdef PTHREADS
+ pthread_mutex_init(&emutex,NULL);
+ #endif
+
return 0;
}
int moldyn_shutdown(t_moldyn *moldyn) {
+ #ifdef PTHREADS
+ int i;
+ #endif
+
printf("[moldyn] shutdown\n");
+ #ifdef PTHREADS
+ for(i=0;i<moldyn->count;i++)
+ pthread_mutex_destroy(&(amutex[i]));
+ free(amutex);
+ pthread_mutex_destroy(&emutex);
+ #endif
+
moldyn_log_shutdown(moldyn);
link_cell_shutdown(moldyn);
rand_close(&(moldyn->random));
switch(type) {
case MOLDYN_POTENTIAL_TM:
- moldyn->func_i0=tersoff_mult_1bp;
- moldyn->func_j1=tersoff_mult_3bp_j1;
- moldyn->func_j1_k0=tersoff_mult_3bp_k1;
- moldyn->func_j1c=tersoff_mult_3bp_j2;
- moldyn->func_j1_k1=tersoff_mult_3bp_k2;
+ //moldyn->func1b=tersoff_mult_1bp;
+ moldyn->func3b_j1=tersoff_mult_3bp_j1;
+ moldyn->func3b_k1=tersoff_mult_3bp_k1;
+ moldyn->func3b_j2=tersoff_mult_3bp_j2;
+ moldyn->func3b_k2=tersoff_mult_3bp_k2;
moldyn->check_2b_bond=tersoff_mult_check_2b_bond;
break;
+ case MOLDYN_POTENTIAL_AO:
+ moldyn->func_j1=albe_orig_mult_3bp_j1;
+ moldyn->func_j1_k0=albe_orig_mult_3bp_k1;
+ moldyn->func_j1c=albe_orig_mult_3bp_j2;
+ moldyn->func_j1_k1=albe_orig_mult_3bp_k2;
+ moldyn->check_2b_bond=albe_orig_mult_check_2b_bond;
+ break;
case MOLDYN_POTENTIAL_AM:
- moldyn->func3b_j1=albe_mult_3bp_j1;
- moldyn->func3b_k1=albe_mult_3bp_k1;
- moldyn->func3b_j2=albe_mult_3bp_j2;
- moldyn->func3b_k2=albe_mult_3bp_k2;
+ moldyn->func_i0=albe_mult_i0;
+ moldyn->func_j0=albe_mult_i0_j0;
+ moldyn->func_j0_k0=albe_mult_i0_j0_k0;
+ moldyn->func_j0e=albe_mult_i0_j1;
+ moldyn->func_j1=albe_mult_i0_j2;
+ moldyn->func_j1_k0=albe_mult_i0_j2_k0;
+ moldyn->func_j1c=albe_mult_i0_j3;
moldyn->check_2b_bond=albe_mult_check_2b_bond;
break;
case MOLDYN_POTENTIAL_HO:
- moldyn->func2b=harmonic_oscillator;
+ moldyn->func_j0=harmonic_oscillator;
moldyn->check_2b_bond=harmonic_oscillator_check_2b_bond;
break;
case MOLDYN_POTENTIAL_LJ:
- moldyn->func2b=lennard_jones;
+ moldyn->func_j0=lennard_jones;
moldyn->check_2b_bond=lennard_jones_check_2b_bond;
break;
default:
* 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,t_3dvec *origin) {
+ int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,
+ u8 attr,u8 brand,int a,int b,int c,t_3dvec *origin,
+ t_part_params *p_params,t_defect_params *d_params,
+ t_offset_params *o_params) {
int new,count;
int ret;
void *ptr;
t_atom *atom;
char name[16];
+ #ifdef PTHREADS
+ pthread_mutex_t *mutex;
+ #endif
new=a*b*c;
count=moldyn->count;
/* how many atoms do we expect */
+ if(type==NONE) {
+ new*=1;
+ printf("[moldyn] WARNING: create 'none' lattice called");
+ }
if(type==CUBIC) new*=1;
if(type==FCC) new*=4;
if(type==DIAMOND) new*=8;
+ /* defects */
+ if(d_params->type) {
+ switch(d_params->stype) {
+ case DEFECT_STYPE_DB_X:
+ case DEFECT_STYPE_DB_Y:
+ case DEFECT_STYPE_DB_Z:
+ case DEFECT_STYPE_DB_R:
+ new*=2;
+ break;
+ default:
+ printf("[moldyn] WARNING: cl unknown defect\n");
+ break;
+ }
+ }
+
/* allocate space for atoms */
ptr=realloc(moldyn->atom,(count+new)*sizeof(t_atom));
if(!ptr) {
moldyn->atom=ptr;
atom=&(moldyn->atom[count]);
+ #ifdef PTHREADS
+ ptr=realloc(amutex,(count+new)*sizeof(pthread_mutex_t));
+ if(!ptr) {
+ perror("[moldyn] mutex realloc (add atom)");
+ return -1;
+ }
+ amutex=ptr;
+ mutex=&(amutex[count]);
+ #endif
+
/* no atoms on the boundaries (only reason: it looks better!) */
if(!origin) {
orig.x=0.5*lc;
switch(type) {
case CUBIC:
+ if(o_params->use)
+ v3_add(&orig,&orig,&(o_params->o));
set_nn_dist(moldyn,lc);
- ret=cubic_init(a,b,c,lc,atom,&orig);
+ ret=cubic_init(a,b,c,lc,atom,&orig,p_params,d_params);
strcpy(name,"cubic");
break;
case FCC:
if(!origin)
v3_scale(&orig,&orig,0.5);
+ if(o_params->use)
+ v3_add(&orig,&orig,&(o_params->o));
set_nn_dist(moldyn,0.5*sqrt(2.0)*lc);
- ret=fcc_init(a,b,c,lc,atom,&orig);
+ ret=fcc_init(a,b,c,lc,atom,&orig,p_params,d_params);
strcpy(name,"fcc");
break;
case DIAMOND:
if(!origin)
v3_scale(&orig,&orig,0.25);
+ if(o_params->use)
+ v3_add(&orig,&orig,&(o_params->o));
set_nn_dist(moldyn,0.25*sqrt(3.0)*lc);
- ret=diamond_init(a,b,c,lc,atom,&orig);
+ ret=diamond_init(a,b,c,lc,atom,&orig,p_params,d_params);
strcpy(name,"diamond");
break;
default:
/* debug */
if(ret!=new) {
- printf("[moldyn] creating lattice failed\n");
+ printf("[moldyn] creating %s lattice (lc=%f) incomplete\n",
+ name,lc);
+ printf(" (ignore for partial lattice creation)\n");
printf(" amount of atoms\n");
printf(" - expected: %d\n",new);
printf(" - created: %d\n",ret);
+ }
+
+ moldyn->count+=ret;
+ if(ret==new)
+ printf("[moldyn] created %s lattice with %d atoms\n",name,ret);
+
+ for(new=0;new<ret;new++) {
+ atom[new].element=element;
+ atom[new].mass=pse_mass[element];
+ atom[new].attr=attr;
+ atom[new].brand=brand;
+ atom[new].tag=count+new;
+ check_per_bound(moldyn,&(atom[new].r));
+ atom[new].r_0=atom[new].r;
+ #ifdef PTHREADS
+ pthread_mutex_init(&(mutex[new]),NULL);
+ #endif
+ if(d_params->type) {
+ new+=1;
+ atom[new].element=d_params->element;
+ atom[new].mass=pse_mass[d_params->element];
+ atom[new].attr=d_params->attr;
+ atom[new].brand=d_params->brand;
+ atom[new].tag=count+new;
+ check_per_bound(moldyn,&(atom[new].r));
+ atom[new].r_0=atom[new].r;
+ #ifdef PTHREADS
+ pthread_mutex_init(&(mutex[new]),NULL);
+ #endif
+ }
+ }
+
+ /* fix allocation */
+ ptr=realloc(moldyn->atom,moldyn->count*sizeof(t_atom));
+ if(!ptr) {
+ perror("[moldyn] realloc (create lattice - alloc fix)");
return -1;
}
+ moldyn->atom=ptr;
- moldyn->count+=new;
- printf("[moldyn] created %s lattice with %d atoms\n",name,new);
+ // WHAT ABOUT AMUTEX !!!!
- for(ret=0;ret<new;ret++) {
- atom[ret].element=element;
- atom[ret].mass=mass;
- atom[ret].attr=attr;
- atom[ret].brand=brand;
- atom[ret].tag=count+ret;
- check_per_bound(moldyn,&(atom[ret].r));
- atom[ret].r_0=atom[ret].r;
+ #ifdef LOWMEM_LISTS
+ ptr=realloc(moldyn->lc.subcell->list,moldyn->count*sizeof(int));
+ if(!ptr) {
+ perror("[moldyn] list realloc (create lattice)");
+ return -1;
}
+ moldyn->lc.subcell->list=ptr;
+ #endif
/* update total system mass */
total_mass_calc(moldyn);
return ret;
}
- int add_atom(t_moldyn *moldyn,int element,double mass,u8 brand,u8 attr,
+ int add_atom(t_moldyn *moldyn,int element,u8 brand,u8 attr,
t_3dvec *r,t_3dvec *v) {
t_atom *atom;
}
moldyn->atom=ptr;
+ #ifdef LOWMEM_LISTS
+ ptr=realloc(moldyn->lc.subcell->list,(count+1)*sizeof(int));
+ if(!ptr) {
+ perror("[moldyn] list realloc (add atom)");
+ return -1;
+ }
+ moldyn->lc.subcell->list=ptr;
+ #endif
+
+ #ifdef PTHREADS
+ ptr=realloc(amutex,(count+1)*sizeof(pthread_mutex_t));
+ if(!ptr) {
+ perror("[moldyn] mutex realloc (add atom)");
+ return -1;
+ }
+ amutex=ptr;
+ pthread_mutex_init(&(amutex[count]),NULL);
+ #endif
+
atom=moldyn->atom;
/* initialize new atom */
atom[count].r=*r;
atom[count].v=*v;
atom[count].element=element;
- atom[count].mass=mass;
+ atom[count].mass=pse_mass[element];
atom[count].brand=brand;
atom[count].tag=count;
atom[count].attr=attr;
t_atom *new,*old;
int cnt;
+ #if defined LOWMEM_LISTS || defined PTHREADS
+ void *ptr;
+ #endif
old=moldyn->atom;
free(old);
+ #ifdef LOWMEM_LISTS
+ ptr=realloc(moldyn->lc.subcell->list,moldyn->count*sizeof(int));
+ if(!ptr) {
+ perror("[moldyn] list realloc (del atom)");
+ return -1;
+ }
+ moldyn->lc.subcell->list=ptr;
+ // update lists
+ link_cell_update(moldyn);
+ #endif
+
+ #ifdef PTHREADS
+ ptr=realloc(amutex,moldyn->count*sizeof(pthread_mutex_t));
+ if(!ptr) {
+ perror("[moldyn] mutex realloc (add atom)");
+ return -1;
+ }
+ amutex=ptr;
+ pthread_mutex_destroy(&(amutex[moldyn->count+1]));
+ #endif
+
+
return 0;
}
+ #define set_atom_positions(pos) \
+ if(d_params->type) {\
+ d_o.x=0; d_o.y=0; d_o.z=0;\
+ d_d.x=0; d_d.y=0; d_d.z=0;\
+ switch(d_params->stype) {\
+ case DEFECT_STYPE_DB_X:\
+ d_o.x=d_params->od;\
+ d_d.x=d_params->dd;\
+ break;\
+ case DEFECT_STYPE_DB_Y:\
+ d_o.y=d_params->od;\
+ d_d.y=d_params->dd;\
+ break;\
+ case DEFECT_STYPE_DB_Z:\
+ d_o.z=d_params->od;\
+ d_d.z=d_params->dd;\
+ break;\
+ case DEFECT_STYPE_DB_R:\
+ break;\
+ default:\
+ printf("[moldyn] WARNING: unknown defect\n");\
+ break;\
+ }\
+ v3_add(&dr,&pos,&d_o);\
+ v3_copy(&(atom[count].r),&dr);\
+ count+=1;\
+ v3_add(&dr,&pos,&d_d);\
+ v3_copy(&(atom[count].r),&dr);\
+ count+=1;\
+ }\
+ else {\
+ v3_copy(&(atom[count].r),&pos);\
+ count+=1;\
+ }
+
/* cubic init */
- int cubic_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin) {
+ int cubic_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin,
+ t_part_params *p_params,t_defect_params *d_params) {
int count;
t_3dvec r;
int i,j,k;
t_3dvec o;
+ t_3dvec dist;
+ t_3dvec p;
+ t_3dvec d_o;
+ t_3dvec d_d;
+ t_3dvec dr;
+
+ p.x=0; p.y=0; p.z=0;
count=0;
if(origin)
else
v3_zero(&o);
+ /* shift partition values */
+ if(p_params->type) {
+ p.x=p_params->p.x+(a*lc)/2.0;
+ p.y=p_params->p.y+(b*lc)/2.0;
+ p.z=p_params->p.z+(c*lc)/2.0;
+ }
+
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;
+ switch(p_params->type) {
+ case PART_INSIDE_R:
+ v3_sub(&dist,&r,&p);
+ if(v3_absolute_square(&dist)<
+ (p_params->r*p_params->r)) {
+ set_atom_positions(r);
+ }
+ break;
+ case PART_OUTSIDE_R:
+ v3_sub(&dist,&r,&p);
+ if(v3_absolute_square(&dist)>=
+ (p_params->r*p_params->r)) {
+ set_atom_positions(r);
+ }
+ break;
+ case PART_INSIDE_D:
+ v3_sub(&dist,&r,&p);
+ if((fabs(dist.x)<p_params->d.x)&&
+ (fabs(dist.y)<p_params->d.y)&&
+ (fabs(dist.z)<p_params->d.z)) {
+ set_atom_positions(r);
+ }
+ break;
+ case PART_OUTSIDE_D:
+ v3_sub(&dist,&r,&p);
+ if((fabs(dist.x)>=p_params->d.x)||
+ (fabs(dist.y)>=p_params->d.y)||
+ (fabs(dist.z)>=p_params->d.z)) {
+ set_atom_positions(r);
+ }
+ break;
+ default:
+ set_atom_positions(r);
+ break;
+ }
r.z+=lc;
}
r.y+=lc;
}
/* fcc lattice init */
- int fcc_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin) {
+ int fcc_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin,
+ t_part_params *p_params,t_defect_params *d_params) {
int count;
int i,j,k,l;
t_3dvec o,r,n;
t_3dvec basis[3];
+ t_3dvec dist;
+ t_3dvec p;
+ t_3dvec d_d,d_o,dr;
+
+ p.x=0; p.y=0; p.z=0;
count=0;
if(origin)
basis[2].y=0.5*lc;
basis[2].z=0.5*lc;
+ /* shift partition values */
+ if(p_params->type) {
+ p.x=p_params->p.x+(a*lc)/2.0;
+ p.y=p_params->p.y+(b*lc)/2.0;
+ p.z=p_params->p.z+(c*lc)/2.0;
+ }
+
/* fill up the room */
r.x=o.x;
for(i=0;i<a;i++) {
r.z=o.z;
for(k=0;k<c;k++) {
/* first atom */
- v3_copy(&(atom[count].r),&r);
- count+=1;
- r.z+=lc;
+ switch(p_params->type) {
+ case PART_INSIDE_R:
+ v3_sub(&dist,&r,&p);
+ if(v3_absolute_square(&dist)<
+ (p_params->r*p_params->r)) {
+ set_atom_positions(r);
+ }
+ break;
+ case PART_OUTSIDE_R:
+ v3_sub(&dist,&r,&p);
+ if(v3_absolute_square(&dist)>=
+ (p_params->r*p_params->r)) {
+ set_atom_positions(r);
+ }
+ break;
+ case PART_INSIDE_D:
+ v3_sub(&dist,&r,&p);
+ if((fabs(dist.x)<p_params->d.x)&&
+ (fabs(dist.y)<p_params->d.y)&&
+ (fabs(dist.z)<p_params->d.z)) {
+ set_atom_positions(r);
+ }
+ break;
+ case PART_OUTSIDE_D:
+ v3_sub(&dist,&r,&p);
+ if((fabs(dist.x)>=p_params->d.x)||
+ (fabs(dist.y)>=p_params->d.y)||
+ (fabs(dist.z)>=p_params->d.z)) {
+ set_atom_positions(r);
+ }
+ break;
+ default:
+ set_atom_positions(r);
+ break;
+ }
/* the three face centered atoms */
for(l=0;l<3;l++) {
v3_add(&n,&r,&basis[l]);
- v3_copy(&(atom[count].r),&n);
- count+=1;
+ switch(p_params->type) {
+ case PART_INSIDE_R:
+ v3_sub(&dist,&n,&p);
+ if(v3_absolute_square(&dist)<
+ (p_params->r*p_params->r)) {
+ set_atom_positions(n);
+ }
+ break;
+ case PART_OUTSIDE_R:
+ v3_sub(&dist,&n,&p);
+ if(v3_absolute_square(&dist)>=
+ (p_params->r*p_params->r)) {
+ set_atom_positions(n);
+ }
+ break;
+ case PART_INSIDE_D:
+ v3_sub(&dist,&n,&p);
+ if((fabs(dist.x)<p_params->d.x)&&
+ (fabs(dist.y)<p_params->d.y)&&
+ (fabs(dist.z)<p_params->d.z)) {
+ set_atom_positions(n);
+ }
+ break;
+ case PART_OUTSIDE_D:
+ v3_sub(&dist,&n,&p);
+ if((fabs(dist.x)>=p_params->d.x)||
+ (fabs(dist.y)>=p_params->d.y)||
+ (fabs(dist.z)>=p_params->d.z)) {
+ set_atom_positions(n);
+ }
+ break;
+ default:
+ set_atom_positions(n);
+ break;
+ }
}
+ r.z+=lc;
}
r.y+=lc;
}
return count;
}
- int diamond_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin) {
+ int diamond_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin,
+ t_part_params *p_params,t_defect_params *d_params) {
int count;
t_3dvec o;
- count=fcc_init(a,b,c,lc,atom,origin);
+ count=fcc_init(a,b,c,lc,atom,origin,p_params,d_params);
o.x=0.25*lc;
o.y=0.25*lc;
if(origin) v3_add(&o,&o,origin);
- count+=fcc_init(a,b,c,lc,&atom[count],&o);
+ count+=fcc_init(a,b,c,lc,&atom[count],&o,p_params,d_params);
return count;
}
/* 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);
+ if(moldyn->count)
+ moldyn->t=(2.0*moldyn->ekin)/(3.0*K_BOLTZMANN*moldyn->count);
+ else moldyn->t=0.0;
return moldyn->t;
}
scale*=2.0;
else
if(moldyn->pt_scale&T_SCALE_BERENDSEN)
- scale=1.0+(scale-1.0)/moldyn->t_tc;
+ scale=1.0+(scale-1.0)*moldyn->tau/moldyn->t_tc;
scale=sqrt(scale);
/* velocity scaling */
}
/* global virial (absolute coordinates) */
- virial=&(moldyn->gvir);
- moldyn->gv=virial->xx+virial->yy+virial->zz;
+ //virial=&(moldyn->gvir);
+ //moldyn->gv=virial->xx+virial->yy+virial->zz;
return moldyn->virial;
}
moldyn->p=2.0*moldyn->ekin+moldyn->virial;
moldyn->p/=(3.0*moldyn->volume);
+ //moldyn->px=2.0*moldyn->ekinx+moldyn->vir.xx;
+ //moldyn->px/=moldyn->volume;
+ //moldyn->py=2.0*moldyn->ekiny+moldyn->vir.yy;
+ //moldyn->py/=moldyn->volume;
+ //moldyn->pz=2.0*moldyn->ekinz+moldyn->vir.zz;
+ //moldyn->pz/=moldyn->volume;
+
/* pressure (absolute coordinates) */
- moldyn->gp=2.0*moldyn->ekin+moldyn->gv;
- moldyn->gp/=(3.0*moldyn->volume);
+ //moldyn->gp=2.0*moldyn->ekin+moldyn->gv;
+ //moldyn->gp/=(3.0*moldyn->volume);
return moldyn->p;
}
/* virial */
moldyn->virial_sum=0.0;
- moldyn->gv_sum=0.0;
+ //moldyn->gv_sum=0.0;
/* pressure */
moldyn->p_sum=0.0;
- moldyn->gp_sum=0.0;
+ //moldyn->gp_sum=0.0;
moldyn->tp_sum=0.0;
return 0;
/* virial */
moldyn->virial_sum+=moldyn->virial;
moldyn->virial_avg=moldyn->virial_sum/denom;
- moldyn->gv_sum+=moldyn->gv;
- moldyn->gv_avg=moldyn->gv_sum/denom;
+ //moldyn->gv_sum+=moldyn->gv;
+ //moldyn->gv_avg=moldyn->gv_sum/denom;
/* pressure */
moldyn->p_sum+=moldyn->p;
moldyn->p_avg=moldyn->p_sum/denom;
- moldyn->gp_sum+=moldyn->gp;
- moldyn->gp_avg=moldyn->gp_sum/denom;
+ //moldyn->gp_sum+=moldyn->gp;
+ //moldyn->gp_avg=moldyn->gp_sum/denom;
moldyn->tp_sum+=moldyn->tp;
moldyn->tp_avg=moldyn->tp_sum/denom;
return 0;
}
+ int scale_atoms_ind(t_moldyn *moldyn,double x,double y,double z) {
+
+ int i;
+ t_3dvec *r;
+
+ for(i=0;i<moldyn->count;i++) {
+ r=&(moldyn->atom[i].r);
+ r->x*=x;
+ r->y*=y;
+ r->z*=z;
+ }
+
+ return 0;
+ }
+
+ int scale_dim_ind(t_moldyn *moldyn,double x,double y,double z) {
+
+ t_3dvec *dim;
+
+ dim=&(moldyn->dim);
+
+ dim->x*=x;
+ dim->y*=y;
+ dim->z*=z;
+
+ return 0;
+ }
+
int scale_volume(t_moldyn *moldyn) {
t_3dvec *dim,*vdim;
double scale;
t_linkcell *lc;
+ //double sx,sy,sz;
vdim=&(moldyn->vis.dim);
dim=&(moldyn->dim);
/* scaling factor */
if(moldyn->pt_scale&P_SCALE_BERENDSEN) {
- scale=1.0-(moldyn->p_ref-moldyn->p)*moldyn->p_tc;
+ scale=1.0-(moldyn->p_ref-moldyn->p)*moldyn->p_tc*moldyn->tau;
scale=pow(scale,ONE_THIRD);
}
else {
scale=pow(moldyn->p/moldyn->p_ref,ONE_THIRD);
}
+
+ /*
+ sx=1.0-(moldyn->p_ref-moldyn->px)*moldyn->p_tc*moldyn->tau;
+ sy=1.0-(moldyn->p_ref-moldyn->py)*moldyn->p_tc*moldyn->tau;
+ sz=1.0-(moldyn->p_ref-moldyn->pz)*moldyn->p_tc*moldyn->tau;
+ sx=pow(sx,ONE_THIRD);
+ sy=pow(sy,ONE_THIRD);
+ sz=pow(sz,ONE_THIRD);
+ */
+
/* scale the atoms and dimensions */
scale_atoms(moldyn,SCALE_DIRECT,scale,TRUE,TRUE,TRUE);
scale_dim(moldyn,SCALE_DIRECT,scale,TRUE,TRUE,TRUE);
+ //scale_atoms_ind(moldyn,sx,sy,sz);
+ //scale_dim_ind(moldyn,sx,sy,sz);
/* visualize dimensions */
if(vdim->x!=0) {
lc->x*=scale;
lc->y*=scale;
lc->z*=scale;
+ //lc->x*=sx;
+ //lc->y*=sx;
+ //lc->z*=sy;
}
return 0;
atom=moldyn->atom;
moldyn->ekin=0.0;
+ //moldyn->ekinx=0.0;
+ //moldyn->ekiny=0.0;
+ //moldyn->ekinz=0.0;
for(i=0;i<moldyn->count;i++) {
atom[i].ekin=0.5*atom[i].mass*v3_absolute_square(&(atom[i].v));
moldyn->ekin+=atom[i].ekin;
+ //moldyn->ekinx+=0.5*atom[i].mass*atom[i].v.x*atom[i].v.x;
+ //moldyn->ekiny+=0.5*atom[i].mass*atom[i].v.y*atom[i].v.y;
+ //moldyn->ekinz+=0.5*atom[i].mass*atom[i].v.z*atom[i].v.z;
}
return moldyn->ekin;
int link_cell_init(t_moldyn *moldyn,u8 vol) {
t_linkcell *lc;
+ #ifndef LOWMEM_LISTS
int i;
+ #endif
lc=&(moldyn->lc);
#ifdef STATIC_LISTS
lc->subcell=malloc(lc->cells*sizeof(int*));
+ #elif LOWMEM_LISTS
+ lc->subcell=malloc(sizeof(t_lowmem_list));
#else
lc->subcell=malloc(lc->cells*sizeof(t_list));
#endif
}
if(lc->cells<27)
- printf("[moldyn] FATAL: less then 27 subcells!\n");
+ printf("[moldyn] FATAL: less then 27 subcells! (%d)\n",
+ lc->cells);
if(vol) {
#ifdef STATIC_LISTS
printf("[moldyn] initializing 'static' linked cells (%d)\n",
lc->cells);
+ #elif LOWMEM_LISTS
+ printf("[moldyn] initializing 'lowmem' linked cells (%d)\n",
+ lc->cells);
#else
printf("[moldyn] initializing 'dynamic' linked cells (%d)\n",
lc->cells);
i,lc->subcell[0],lc->subcell);
*/
}
+ #elif LOWMEM_LISTS
+ lc->subcell->head=malloc(lc->cells*sizeof(int));
+ if(lc->subcell->head==NULL) {
+ perror("[moldyn] head init (malloc)");
+ return -1;
+ }
+ lc->subcell->list=malloc(moldyn->count*sizeof(int));
+ if(lc->subcell->list==NULL) {
+ perror("[moldyn] list init (malloc)");
+ return -1;
+ }
#else
for(i=0;i<lc->cells;i++)
list_init_f(&(lc->subcell[i]));
int link_cell_update(t_moldyn *moldyn) {
int count,i,j,k;
- int nx,ny;
+ int nx,nxy;
t_atom *atom;
t_linkcell *lc;
#ifdef STATIC_LISTS
int p;
+ #elif LOWMEM_LISTS
+ int p;
#endif
atom=moldyn->atom;
lc=&(moldyn->lc);
nx=lc->nx;
- ny=lc->ny;
+ nxy=nx*lc->ny;
for(i=0;i<lc->cells;i++)
#ifdef STATIC_LISTS
- memset(lc->subcell[i],0,(MAX_ATOMS_PER_LIST+1)*sizeof(int));
+ memset(lc->subcell[i],-1,(MAX_ATOMS_PER_LIST+1)*sizeof(int));
+ #elif LOWMEM_LISTS
+ lc->subcell->head[i]=-1;
#else
list_destroy_f(&(lc->subcell[i]));
#endif
#ifdef STATIC_LISTS
p=0;
- while(lc->subcell[i+j*nx+k*nx*ny][p]!=0)
+ while(lc->subcell[i+j*nx+k*nxy][p]!=-1)
p++;
if(p>=MAX_ATOMS_PER_LIST) {
return -1;
}
- lc->subcell[i+j*nx+k*nx*ny][p]=count;
+ lc->subcell[i+j*nx+k*nxy][p]=count;
+ #elif LOWMEM_LISTS
+ p=i+j*nx+k*nxy;
+ lc->subcell->list[count]=lc->subcell->head[p];
+ lc->subcell->head[p]=count;
#else
- list_add_immediate_f(&(lc->subcell[i+j*nx+k*nx*ny]),
+ list_add_immediate_f(&(lc->subcell[i+j*nx+k*nxy]),
&(atom[count]));
/*
if(j==0&&k==0)
int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,
#ifdef STATIC_LISTS
int **cell
+ #elif LOWMEM_LISTS
+ int *cell
#else
t_list *cell
#endif
printf("[moldyn] WARNING: lcni %d/%d %d/%d %d/%d\n",
i,nx,j,ny,k,nz);
+ #ifndef LOWMEM_LISTS
cell[0]=lc->subcell[i+j*nx+k*a];
+ #else
+ cell[0]=lc->subcell->head[i+j*nx+k*a];
+ #endif
for(ci=-1;ci<=1;ci++) {
bx=0;
x=i+ci;
}
if(!(ci|cj|ck)) continue;
if(bx|by|bz) {
+ #ifndef LOWMEM_LISTS
cell[--count2]=lc->subcell[x+y*nx+z*a];
+ #else
+ cell[--count2]=lc->subcell->head[x+y*nx+z*a];
+ #endif
+
}
else {
+ #ifndef LOWMEM_LISTS
cell[count1++]=lc->subcell[x+y*nx+z*a];
+ #else
+ cell[count1++]=lc->subcell->head[x+y*nx+z*a];
+ #endif
}
}
}
int link_cell_shutdown(t_moldyn *moldyn) {
+ #ifndef LOWMEM_LISTS
int i;
+ #endif
t_linkcell *lc;
lc=&(moldyn->lc);
+ #if LOWMEM_LISTS
+ free(lc->subcell->head);
+ free(lc->subcell->list);
+
+ #else
+
for(i=0;i<lc->cells;i++) {
#ifdef STATIC_LISTS
free(lc->subcell[i]);
list_destroy_f(&(lc->subcell[i]));
#endif
}
+ #endif
free(lc->subcell);
struct timeval t1,t2;
//double tp;
+ #ifdef VISUAL_THREAD
+ u8 first,change;
+ pthread_t io_thread;
+ int ret;
+ t_moldyn md_copy;
+ t_atom *atom_copy;
+
+ first=1;
+ change=0;
+ #endif
+
sched=&(moldyn->schedule);
atom=moldyn->atom;
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)
+ if(moldyn->count) {
+ 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 */
// should have right values!
/* debugging, ignore */
moldyn->debug=0;
+ /* zero & init moldyn copy */
+ #ifdef VISUAL_THREAD
+ memset(&md_copy,0,sizeof(t_moldyn));
+ atom_copy=malloc(moldyn->count*sizeof(t_atom));
+ if(atom_copy==NULL) {
+ perror("[moldyn] malloc atom copy (init)");
+ return -1;
+ }
+ #endif
+
+ #ifdef PTHREADS
+ printf("##################\n");
+ printf("# USING PTHREADS #\n");
+ printf("##################\n");
+ #endif
/* tell the world */
printf("[moldyn] integration start, go get a coffee ...\n");
temperature_calc(moldyn);
virial_sum(moldyn);
pressure_calc(moldyn);
- /*
+ #ifdef PDEBUG
thermodynamic_pressure_calc(moldyn);
printf("\n\nDEBUG: numeric pressure calc: %f\n\n",
moldyn->tp/BAR);
- */
+ #endif
/* calculate fluctuations + averages */
average_and_fluctuation_calc(moldyn);
if(e) {
if(!(moldyn->total_steps%e))
dprintf(moldyn->efd,
- "%f %f %f %f\n",
+ "%f %f %f %f %f %f\n",
moldyn->time,moldyn->ekin/energy_scale,
moldyn->energy/energy_scale,
- get_total_energy(moldyn)/energy_scale);
+ get_total_energy(moldyn)/energy_scale,
+ moldyn->ekin/EV,moldyn->energy/EV);
}
if(m) {
if(!(moldyn->total_steps%m)) {
dprintf(moldyn->pfd,
"%f %f %f %f %f %f %f\n",moldyn->time,
moldyn->p/BAR,moldyn->p_avg/BAR,
- moldyn->gp/BAR,moldyn->gp_avg/BAR,
+ moldyn->p/BAR,moldyn->p_avg/BAR,
moldyn->tp/BAR,moldyn->tp_avg/BAR);
}
}
if(v) {
if(!(moldyn->total_steps%v)) {
dprintf(moldyn->vfd,
- "%f %f\n",moldyn->time,moldyn->volume);
+ "%f %f %f %f %f\n",moldyn->time,
+ moldyn->volume,
+ moldyn->dim.x,
+ moldyn->dim.y,
+ moldyn->dim.z);
}
}
if(s) {
if(!(moldyn->total_steps%s)) {
- snprintf(dir,128,"%s/s-%07.f.save",
+ snprintf(dir,128,"%s/s-%08.f.save",
moldyn->vlsdir,moldyn->time);
fd=open(dir,O_WRONLY|O_TRUNC|O_CREAT,
S_IRUSR|S_IWUSR);
}
if(a) {
if(!(moldyn->total_steps%a)) {
+ #ifdef VISUAL_THREAD
+ /* check whether thread has not terminated yet */
+ if(!first) {
+ ret=pthread_join(io_thread,NULL);
+ }
+ first=0;
+ /* prepare and start thread */
+ if(moldyn->count!=md_copy.count) {
+ free(atom_copy);
+ change=1;
+ }
+ memcpy(&md_copy,moldyn,sizeof(t_moldyn));
+ if(change) {
+ atom_copy=malloc(moldyn->count*sizeof(t_atom));
+ if(atom_copy==NULL) {
+ perror("[moldyn] malloc atom copy (change)");
+ return -1;
+ }
+ }
+ md_copy.atom=atom_copy;
+ memcpy(atom_copy,moldyn->atom,moldyn->count*sizeof(t_atom));
+ change=0;
+ ret=pthread_create(&io_thread,NULL,visual_atoms,&md_copy);
+ if(ret) {
+ perror("[moldyn] create visual atoms thread\n");
+ return -1;
+ }
+ #else
visual_atoms(moldyn);
+ #endif
}
}
/* display progress */
- //if(!(moldyn->total_steps%10)) {
+ #ifndef PDEBUG
+ if(!(i%10)) {
+ #endif
/* get current time */
gettimeofday(&t2,NULL);
- printf("\rsched:%d, steps:%d/%d, T:%4.1f/%4.1f P:%4.1f/%4.1f V:%6.1f (%d)",
+ printf("sched:%d, steps:%d/%d, T:%4.1f/%4.1f P:%4.1f/%4.1f V:%6.1f (%d)\n",
sched->count,i,moldyn->total_steps,
moldyn->t,moldyn->t_avg,
+ #ifndef PDEBUG
moldyn->p/BAR,moldyn->p_avg/BAR,
- //moldyn->p/BAR,(moldyn->p-2.0*moldyn->ekin/(3.0*moldyn->volume))/BAR,
+ #else
+ moldyn->p/BAR,(moldyn->p-2.0*moldyn->ekin/(3.0*moldyn->volume))/BAR,
+ #endif
moldyn->volume,
(int)(t2.tv_sec-t1.tv_sec));
/* copy over time */
t1=t2;
- //}
+ #ifndef PDEBUG
+ }
+ #endif
/* increase absolute time */
moldyn->time+=moldyn->tau;
}
+ /* writing a final save file! */
+ if(s) {
+ snprintf(dir,128,"%s/s-final.save",moldyn->vlsdir);
+ fd=open(dir,O_WRONLY|O_TRUNC|O_CREAT,S_IRUSR|S_IWUSR);
+ if(fd<0) perror("[moldyn] save fd open");
+ else {
+ write(fd,moldyn,sizeof(t_moldyn));
+ write(fd,moldyn->atom,
+ moldyn->count*sizeof(t_atom));
+ }
+ close(fd);
+ }
+ /* writing a final visual file! */
+ if(a)
+ visual_atoms(moldyn);
+
+ return 0;
+ }
+
+ /* basis trafo */
+
+ #define FORWARD 0
+ #define BACKWARD 1
+
+ int basis_trafo(t_3dvec *r,u8 dir,double z,double x) {
+
+ t_3dvec tmp;
+
+ if(dir==FORWARD) {
+ if(z!=0.0) {
+ v3_copy(&tmp,r);
+ r->x=cos(z)*tmp.x-sin(z)*tmp.y;
+ r->y=sin(z)*tmp.x+cos(z)*tmp.y;
+ }
+ if(x!=0.0) {
+ v3_copy(&tmp,r);
+ r->y=cos(x)*tmp.y-sin(x)*tmp.z;
+ r->z=sin(x)*tmp.y+cos(x)*tmp.z;
+ }
+ }
+ else {
+ if(x!=0.0) {
+ v3_copy(&tmp,r);
+ r->y=cos(-x)*tmp.y-sin(-x)*tmp.z;
+ r->z=sin(-x)*tmp.y+cos(-x)*tmp.z;
+ }
+ if(z!=0.0) {
+ v3_copy(&tmp,r);
+ r->x=cos(-z)*tmp.x-sin(-z)*tmp.y;
+ r->y=sin(-z)*tmp.x+cos(-z)*tmp.y;
+ }
+ }
+
return 0;
}
tau_square=moldyn->tau_square;
for(i=0;i<count;i++) {
+
/* check whether fixed atom */
if(atom[i].attr&ATOM_ATTR_FP)
continue;
+
/* new positions */
h=0.5/atom[i].mass;
+
+ /* constraint relaxation */
+ if(crtt) {
+ // forces
+ basis_trafo(&(atom[i].f),FORWARD,
+ trafo_angle[2*i],trafo_angle[2*i+1]);
+ if(constraints[3*i])
+ atom[i].f.x=0;
+ if(constraints[3*i+1])
+ atom[i].f.y=0;
+ if(constraints[3*i+2])
+ atom[i].f.z=0;
+ basis_trafo(&(atom[i].f),BACKWARD,
+ trafo_angle[2*i],trafo_angle[2*i+1]);
+ // velocities
+ basis_trafo(&(atom[i].v),FORWARD,
+ trafo_angle[2*i],trafo_angle[2*i+1]);
+ if(constraints[3*i])
+ atom[i].v.x=0;
+ if(constraints[3*i+1])
+ atom[i].v.y=0;
+ if(constraints[3*i+2])
+ atom[i].v.z=0;
+ basis_trafo(&(atom[i].v),BACKWARD,
+ trafo_angle[2*i],trafo_angle[2*i+1]);
+ }
+
+ #ifndef QUENCH
v3_scale(&delta,&(atom[i].v),tau);
v3_add(&(atom[i].r),&(atom[i].r),&delta);
+ #endif
v3_scale(&delta,&(atom[i].f),h*tau_square);
v3_add(&(atom[i].r),&(atom[i].r),&delta);
+ //check_per_bound_and_care_for_pbc(moldyn,&(atom[i]));
check_per_bound(moldyn,&(atom[i].r));
/* velocities [actually v(t+tau/2)] */
link_cell_update(moldyn);
/* forces depending on chosen potential */
- potential_force_calc(moldyn);
+ #ifndef ALBE_FAST
+ // if albe, use albe force calc routine
+ //if(moldyn->func3b_j1==albe_mult_3bp_j1)
+ // albe_potential_force_calc(moldyn);
+ //else
+ potential_force_calc(moldyn);
+ #else
+ albe_potential_force_calc(moldyn);
+ #endif
for(i=0;i<count;i++) {
/* check whether fixed atom */
if(atom[i].attr&ATOM_ATTR_FP)
continue;
+
+ /* constraint relaxation */
+ if(crtt) {
+ // forces
+ basis_trafo(&(atom[i].f),FORWARD,
+ trafo_angle[2*i],trafo_angle[2*i+1]);
+ if(constraints[3*i])
+ atom[i].f.x=0;
+ if(constraints[3*i+1])
+ atom[i].f.y=0;
+ if(constraints[3*i+2])
+ atom[i].f.z=0;
+ basis_trafo(&(atom[i].f),BACKWARD,
+ trafo_angle[2*i],trafo_angle[2*i+1]);
+ // velocities
+ basis_trafo(&(atom[i].v),FORWARD,
+ trafo_angle[2*i],trafo_angle[2*i+1]);
+ if(constraints[3*i])
+ atom[i].v.x=0;
+ if(constraints[3*i+1])
+ atom[i].v.y=0;
+ if(constraints[3*i+2])
+ atom[i].v.z=0;
+ basis_trafo(&(atom[i].v),BACKWARD,
+ trafo_angle[2*i],trafo_angle[2*i+1]);
+ }
+
/* 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);
int *neighbour_i[27];
int p,q;
t_atom *atom;
+ #elif LOWMEM_LISTS
+ int neighbour_i[27];
+ int p,q;
#else
t_list neighbour_i[27];
t_list neighbour_i2[27];
memset(&(moldyn->gvir),0,sizeof(t_virial));
/* reset force, site energy and virial of every atom */
+ #ifdef PARALLEL
+ i=omp_get_thread_num();
+ #pragma omp parallel for private(virial)
+ #endif
for(i=0;i<count;i++) {
/* reset force */
/* single particle potential/force */
if(itom[i].attr&ATOM_ATTR_1BP)
- if(moldyn->func1b)
- moldyn->func1b(moldyn,&(itom[i]));
+ if(moldyn->func_i0)
+ moldyn->func_i0(moldyn,&(itom[i]));
if(!(itom[i].attr&(ATOM_ATTR_2BP|ATOM_ATTR_3BP)))
continue;
dnlc=lc->dnlc;
+#ifndef STATIC_LISTS
+ /* check for later 3 body interaction */
+ if(itom[i].attr&ATOM_ATTR_3BP)
+ memcpy(neighbour_i2,neighbour_i,27*sizeof(t_list));
+#endif
+
/* first loop over atoms j */
- if(moldyn->func2b) {
+ if(moldyn->func_j0) {
for(j=0;j<27;j++) {
bc_ij=(j<dnlc)?0:1;
#ifdef STATIC_LISTS
p=0;
- while(neighbour_i[j][p]!=0) {
+ while(neighbour_i[j][p]!=-1) {
jtom=&(atom[neighbour_i[j][p]]);
p++;
+ #elif LOWMEM_LISTS
+ p=neighbour_i[j];
+
+ while(p!=-1) {
+
+ jtom=&(itom[p]);
+ p=lc->subcell->list[p];
#else
this=&(neighbour_i[j]);
list_reset_f(this);
if(jtom==&(itom[i]))
continue;
+ /* reset 3bp run */
+ moldyn->run3bp=1;
+
if((jtom->attr&ATOM_ATTR_2BP)&
(itom[i].attr&ATOM_ATTR_2BP)) {
- moldyn->func2b(moldyn,
- &(itom[i]),
- jtom,
- bc_ij);
+ moldyn->func_j0(moldyn,
+ &(itom[i]),
+ jtom,
+ bc_ij);
+ }
+
+ /* 3 body potential/force */
+
+ /* in j loop, 3bp run can be skipped */
+ if(!(moldyn->run3bp))
+ continue;
+
+ if(!(itom[i].attr&ATOM_ATTR_3BP))
+ continue;
+
+ if(!(jtom->attr&ATOM_ATTR_3BP))
+ continue;
+
+ if(moldyn->func_j0_k0==NULL)
+ continue;
+
+ /* first loop over atoms k in first j loop */
+ for(k=0;k<27;k++) {
+
+ bc_ik=(k<dnlc)?0:1;
+#ifdef STATIC_LISTS
+ q=0;
+
+ while(neighbour_i[j][q]!=0) {
+
+ ktom=&(atom[neighbour_i[k][q]]);
+ q++;
+#else
+ that=&(neighbour_i2[k]);
+ list_reset_f(that);
+
+ if(that->start==NULL)
+ continue;
+
+ do {
+ ktom=that->current->data;
+#endif
+
+ if(!(ktom->attr&ATOM_ATTR_3BP))
+ continue;
+
+ //if(ktom==jtom)
+ // continue;
+
+ if(ktom==&(itom[i]))
+ continue;
+
+ moldyn->func_j0_k0(moldyn,
+ &(itom[i]),
+ jtom,
+ ktom,
+ bc_ik|bc_ij);
+#ifdef STATIC_LISTS
}
- #else
- } while(list_next_f(that)!=\
- L_NO_NEXT_ELEMENT);
- #endif
-
- }
-
- /* finish of first j loop after first k loop */
- if(moldyn->func_j0e)
- moldyn->func_j0e(moldyn,
- &(itom[i]),
- jtom,
- bc_ij);
-
#ifdef STATIC_LISTS
}
+ #elif LOWMEM_LISTS
+ }
#else
} while(list_next_f(this)!=L_NO_NEXT_ELEMENT);
#endif
}
}
- /* 3 body potential/force */
+ /* continued 3 body potential/force */
if(!(itom[i].attr&ATOM_ATTR_3BP))
continue;
+ /* copy the neighbour lists */
+ #ifdef STATIC_LISTS
+ /* no copy needed for static lists */
+ #elif LOWMEM_LISTS
+ /* no copy needed for lowmem lists */
+ #else
+ memcpy(neighbour_i2,neighbour_i,27*sizeof(t_list));
+ #endif
+
/* second loop over atoms j */
for(j=0;j<27;j++) {
#ifdef STATIC_LISTS
p=0;
- while(neighbour_i[j][p]!=0) {
+ while(neighbour_i[j][p]!=-1) {
jtom=&(atom[neighbour_i[j][p]]);
p++;
+ #elif LOWMEM_LISTS
+ p=neighbour_i[j];
+
+ while(p!=-1) {
+
+ jtom=&(itom[p]);
+ p=lc->subcell->list[p];
#else
this=&(neighbour_i[j]);
list_reset_f(this);
/* reset 3bp run */
moldyn->run3bp=1;
- if(moldyn->func3b_j1)
- moldyn->func3b_j1(moldyn,
- &(itom[i]),
- jtom,
- bc_ij);
+ if(moldyn->func_j1)
+ moldyn->func_j1(moldyn,
+ &(itom[i]),
+ jtom,
+ bc_ij);
- /* in first j loop, 3bp run can be skipped */
+ /* in j loop, 3bp run can be skipped */
if(!(moldyn->run3bp))
continue;
- /* first loop over atoms k */
- if(moldyn->func3b_k1) {
+ /* first loop over atoms k in second j loop */
+ if(moldyn->func_j1_k0) {
for(k=0;k<27;k++) {
#ifdef STATIC_LISTS
q=0;
- while(neighbour_i[j][q]!=0) {
+ while(neighbour_i[k][q]!=-1) {
ktom=&(atom[neighbour_i[k][q]]);
q++;
+ #elif LOWMEM_LISTS
+ q=neighbour_i[k];
+
+ while(q!=-1) {
+
+ ktom=&(itom[q]);
+ q=lc->subcell->list[q];
#else
that=&(neighbour_i2[k]);
list_reset_f(that);
if(!(ktom->attr&ATOM_ATTR_3BP))
continue;
- if(ktom==jtom)
- continue;
+ //if(ktom==jtom)
+ // continue;
if(ktom==&(itom[i]))
continue;
- moldyn->func_j1_k0(moldyn,
- &(itom[i]),
- jtom,
- ktom,
- bc_ik|bc_ij);
+ moldyn->func3b_k1(moldyn,
+ &(itom[i]),
+ jtom,
+ ktom,
+ bc_ik|bc_ij);
+
#ifdef STATIC_LISTS
}
+ #elif LOWMEM_LISTS
+ }
#else
} while(list_next_f(that)!=\
L_NO_NEXT_ELEMENT);
}
- if(moldyn->func3b_j2)
- moldyn->func3b_j2(moldyn,
- &(itom[i]),
- jtom,
- bc_ij);
+ /* continued j loop after first k loop */
+ if(moldyn->func_j1c)
+ moldyn->func_j1c(moldyn,
+ &(itom[i]),
+ jtom,
+ bc_ij);
/* second loop over atoms k */
- if(moldyn->func3b_k2) {
+ if(moldyn->func_j1_k1) {
for(k=0;k<27;k++) {
#ifdef STATIC_LISTS
q=0;
- while(neighbour_i[j][q]!=0) {
+ while(neighbour_i[k][q]!=-1) {
ktom=&(atom[neighbour_i[k][q]]);
q++;
+ #elif LOWMEM_LISTS
+ q=neighbour_i[k];
+
+ while(q!=-1) {
+
+ ktom=&(itom[q]);
+ q=lc->subcell->list[q];
#else
that=&(neighbour_i2[k]);
list_reset_f(that);
if(!(ktom->attr&ATOM_ATTR_3BP))
continue;
- if(ktom==jtom)
- continue;
+ //if(ktom==jtom)
+ // continue;
if(ktom==&(itom[i]))
continue;
- moldyn->func3b_k2(moldyn,
- &(itom[i]),
- jtom,
- ktom,
- bc_ik|bc_ij);
+ moldyn->func_j1_k1(moldyn,
+ &(itom[i]),
+ jtom,
+ ktom,
+ bc_ik|bc_ij);
#ifdef STATIC_LISTS
}
+ #elif LOWMEM_LISTS
+ }
#else
} while(list_next_f(that)!=\
L_NO_NEXT_ELEMENT);
}
- /* 2bp post function */
- if(moldyn->func3b_j3) {
- moldyn->func3b_j3(moldyn,
- &(itom[i]),
- jtom,bc_ij);
+ /* finish of j loop after second k loop */
+ if(moldyn->func_j1e) {
+ moldyn->func_j1e(moldyn,
+ &(itom[i]),
+ jtom,bc_ij);
}
#ifdef STATIC_LISTS
}
+ #elif LOWMEM_LISTS
+ }
#else
} while(list_next_f(this)!=L_NO_NEXT_ELEMENT);
#endif
}
-
+
#ifdef DEBUG
//printf("\n\n");
#endif
#endif
/* some postprocessing */
+ #ifdef PARALLEL
+ #pragma omp parallel for
+ #endif
for(i=0;i<count;i++) {
/* calculate global virial */
moldyn->gvir.xx+=itom[i].r.x*itom[i].f.x;
/* check forces regarding the given timestep */
if(v3_norm(&(itom[i].f))>\
- 0.1*moldyn->nnd*itom[i].mass/moldyn->tau_square)
+ 0.1*moldyn->nnd*itom[i].mass/moldyn->tau_square)
printf("[moldyn] WARNING: pfc (high force: atom %d)\n",
i);
}
return 0;
}
+ int check_per_bound_and_care_for_pbc(t_moldyn *moldyn,t_atom *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->r.x>=x) {
+ a->pbc[0]+=1;
+ a->r.x-=dim->x;
+ }
+ else if(-a->r.x>x) {
+ a->pbc[0]-=1;
+ a->r.x+=dim->x;
+ }
+ }
+ if(moldyn->status&MOLDYN_STAT_PBY) {
+ if(a->r.y>=y) {
+ a->pbc[1]+=1;
+ a->r.y-=dim->y;
+ }
+ else if(-a->r.y>y) {
+ a->pbc[1]-=1;
+ a->r.y+=dim->y;
+ }
+ }
+ if(moldyn->status&MOLDYN_STAT_PBZ) {
+ if(a->r.z>=z) {
+ a->pbc[2]+=1;
+ a->r.z-=dim->z;
+ }
+ else if(-a->r.z>z) {
+ a->pbc[2]-=1;
+ a->r.z+=dim->z;
+ }
+ }
+
+ return 0;
+ }
+
/*
* debugging / critical check functions
*/
if(fsize!=sizeof(t_moldyn)+size) {
corr=fsize-sizeof(t_moldyn)-size;
printf("[moldyn] WARNING: lsf (illegal file size)\n");
- printf(" moifying offset:\n");
+ printf(" modifying offset:\n");
printf(" - current pos: %d\n",sizeof(t_moldyn));
printf(" - atom size: %d\n",size);
printf(" - file size: %d\n",fsize);
size-=cnt;
}
+ #ifdef PTHREADS
+ amutex=malloc(moldyn->count*sizeof(pthread_mutex_t));
+ if(amutex==NULL) {
+ perror("[moldyn] load save file (mutexes)");
+ return -1;
+ }
+ for(cnt=0;cnt<moldyn->count;cnt++)
+ pthread_mutex_init(&(amutex[cnt]),NULL);
+ #endif
+
// hooks etc ...
return 0;
#ifdef STATIC_LISTS
int *neighbour[27];
int p;
+ #elif LOWMEM_LISTS
+ int neighbour[27];
+ int p;
#else
t_list neighbour[27];
+ t_list *this;
#endif
u8 bc;
t_atom *itom,*jtom;
int i,j;
- t_list *this;
lc=&(moldyn->lc);
itom=moldyn->atom;
#ifdef STATIC_LISTS
p=0;
- while(neighbour[j][p]!=0) {
+ while(neighbour[j][p]!=-1) {
jtom=&(moldyn->atom[neighbour[j][p]]);
p++;
+ #elif LOWMEM_LISTS
+ p=neighbour[j];
+
+ while(p!=-1) {
+
+ jtom=&(itom[p]);
+ p=lc->subcell->list[p];
#else
this=&(neighbour[j]);
list_reset_f(this);
#ifdef STATIC_LISTS
}
+ #elif LOWMEM_LISTS
+ }
#else
} while(list_next_f(this)!=L_NO_NEXT_ELEMENT);
#endif
}
+ /*
+ * function to find neighboured atoms
+ */
+
+ int process_neighbours(t_moldyn *moldyn,void *data,t_atom *atom,
+ int (*process)(t_moldyn *moldyn,t_atom *atom,t_atom *natom,
+ void *data,u8 bc)) {
+
+ t_linkcell *lc;
+ #ifdef STATIC_LISTS
+ int *neighbour[27];
+ int p;
+ #elif LOWMEM_LISTS
+ int neighbour[27];
+ int p;
+ #else
+ t_list neighbour[27];
+ t_list *this;
+ #endif
+ u8 bc;
+ t_atom *natom;
+ int j;
+
+ lc=&(moldyn->lc);
+
+ /* neighbour indexing */
+ link_cell_neighbour_index(moldyn,
+ (atom->r.x+moldyn->dim.x/2)/lc->x,
+ (atom->r.y+moldyn->dim.y/2)/lc->x,
+ (atom->r.z+moldyn->dim.z/2)/lc->x,
+ neighbour);
+
+ for(j=0;j<27;j++) {
+
+ bc=(j<lc->dnlc)?0:1;
+
+ #ifdef STATIC_LISTS
+ p=0;
+
+ while(neighbour[j][p]!=-1) {
+
+ natom=&(moldyn->atom[neighbour[j][p]]);
+ p++;
+ #elif LOWMEM_LISTS
+ p=neighbour[j];
+
+ while(p!=-1) {
+
+ natom=&(moldyn->atom[p]);
+ p=lc->subcell->list[p];
+ #else
+ this=&(neighbour[j]);
+ list_reset_f(this);
+
+ if(this->start==NULL)
+ continue;
+
+ do {
+
+ natom=this->current->data;
+ #endif
+
+ /* process bond */
+ process(moldyn,atom,natom,data,bc);
+
+ #ifdef STATIC_LISTS
+ }
+ #elif LOWMEM_LISTS
+ }
+ #else
+ } while(list_next_f(this)!=L_NO_NEXT_ELEMENT);
+ #endif
+ }
+
+ return 0;
+
+ }
+
/*
* post processing functions
*/
int i;
t_atom *atom;
t_3dvec dist;
+ t_3dvec final_r;
double d2;
int a_cnt;
int b_cnt;
for(i=0;i<moldyn->count;i++) {
- v3_sub(&dist,&(atom[i].r),&(atom[i].r_0));
- check_per_bound(moldyn,&dist);
+ /* care for pb crossing */
+ final_r.x=atom[i].r.x+atom[i].pbc[0]*moldyn->dim.x;
+ final_r.y=atom[i].r.y+atom[i].pbc[1]*moldyn->dim.y;
+ final_r.z=atom[i].r.z+atom[i].pbc[2]*moldyn->dim.z;
+ /* calculate distance */
+ v3_sub(&dist,&final_r,&(atom[i].r_0));
d2=v3_absolute_square(&dist);
if(atom[i].brand) {
return 0;
}
+ int calculate_msd(t_moldyn *moldyn,double *msd) {
+
+ int i;
+ t_atom *atom;
+ t_3dvec dist;
+ t_3dvec final_r;
+ double d2;
+ int a_cnt;
+ int b_cnt;
+
+ atom=moldyn->atom;
+ msd[0]=0;
+ msd[1]=0;
+ msd[2]=0;
+ a_cnt=0;
+ b_cnt=0;
+
+ for(i=0;i<moldyn->count;i++) {
+
+ /* care for pb crossing */
+ if(atom[i].pbc[0]|atom[i].pbc[1]|atom[i].pbc[2]) {
+ printf("[moldyn] msd pb crossings for atom %d\n",i);
+ printf(" x: %d y: %d z: %d\n",
+ atom[i].pbc[0],atom[i].pbc[1],atom[i].pbc[2]);
+ }
+ final_r.x=atom[i].r.x+atom[i].pbc[0]*moldyn->dim.x;
+ final_r.y=atom[i].r.y+atom[i].pbc[1]*moldyn->dim.y;
+ final_r.z=atom[i].r.z+atom[i].pbc[2]*moldyn->dim.z;
+ /* calculate distance */
+ v3_sub(&dist,&final_r,&(atom[i].r_0));
+ d2=v3_absolute_square(&dist);
+
+ if(atom[i].brand) {
+ b_cnt+=1;
+ msd[1]+=d2;
+ }
+ else {
+ a_cnt+=1;
+ msd[0]+=d2;
+ }
+
+ msd[2]+=d2;
+ }
+
+ msd[0]/=a_cnt;
+ msd[1]/=b_cnt;
+ msd[2]/=moldyn->count;
+
+ return 0;
+ }
+
int bonding_analyze(t_moldyn *moldyn,double *cnt) {
return 0;
ba=data;
/* increase total bond counter
- * ... double counting!
*/
- ba->tcnt+=2;
+ ba->tcnt+=1;
if(itom->brand==0)
ba->acnt[jtom->tag]+=1;
int bond_analyze(t_moldyn *moldyn,double *quality) {
- // by now: # bonds of type 'a-4b' and 'b-4a' / # bonds total
-
- int qcnt;
- int ccnt,cset;
+ int qcnt4;
+ int qcnt3;
+ int ccnt4;
+ int ccnt3;
+ int bcnt;
t_ba ba;
int i;
t_atom *atom;
memset(ba.bcnt,0,moldyn->count*sizeof(int));
ba.tcnt=0;
- qcnt=0;
- ccnt=0;
- cset=0;
+ qcnt4=0; qcnt3=0;
+ ccnt4=0; ccnt3=0;
+ bcnt=0;
atom=moldyn->atom;
for(i=0;i<moldyn->count;i++) {
if(atom[i].brand==0) {
if((ba.acnt[i]==0)&(ba.bcnt[i]==4))
- qcnt+=4;
+ qcnt4+=4;
+ if((ba.acnt[i]==0)&(ba.bcnt[i]==3))
+ qcnt3+=3;
}
else {
if((ba.acnt[i]==4)&(ba.bcnt[i]==0)) {
- qcnt+=4;
- ccnt+=1;
+ qcnt4+=4;
+ ccnt4+=1;
+ }
+ if((ba.acnt[i]==3)&(ba.bcnt[i]==0)) {
+ qcnt3+=4;
+ ccnt3+=1;
}
- cset+=1;
+ bcnt+=1;
}
}
- printf("[moldyn] bond analyze: c_cnt=%d | set=%d\n",ccnt,cset);
- printf("[moldyn] bond analyze: q_cnt=%d | tot=%d\n",qcnt,ba.tcnt);
-
if(quality) {
- quality[0]=1.0*ccnt/cset;
- quality[1]=1.0*qcnt/ba.tcnt;
+ quality[0]=1.0*ccnt4/bcnt;
+ quality[1]=1.0*ccnt3/bcnt;
}
else {
- printf("[moldyn] bond analyze: c_bnd_q=%f\n",1.0*qcnt/ba.tcnt);
- printf("[moldyn] bond analyze: tot_q=%f\n",1.0*qcnt/ba.tcnt);
+ printf("[moldyn] bond analyze: %f %f\n",
+ 1.0*ccnt4/bcnt,1.0*ccnt3/bcnt);
}
return 0;
return 0;
}
+ #ifdef VISUAL_THREAD
+ void *visual_atoms(void *ptr) {
+ #else
int visual_atoms(t_moldyn *moldyn) {
+ #endif
int i;
char file[128+64];
t_visual *v;
t_atom *atom;
t_vb vb;
+ t_3dvec strain;
+ #ifdef VISUAL_THREAD
+ t_moldyn *moldyn;
+
+ moldyn=ptr;
+ #endif
v=&(moldyn->vis);
dim.x=v->dim.x;
help=(dim.x+dim.y);
- sprintf(file,"%s/atomic_conf_%07.f.xyz",v->fb,moldyn->time);
+ sprintf(file,"%s/atomic_conf_%08.f.xyz",v->fb,moldyn->time);
vb.fd=open(file,O_WRONLY|O_CREAT|O_TRUNC,S_IRUSR|S_IWUSR);
if(vb.fd<0) {
perror("open visual save file fd");
+ #ifndef VISUAL_THREAD
return -1;
+ #endif
}
/* write the actual data file */
// povray header
- dprintf(vb.fd,"# [P] %d %07.f <%f,%f,%f>\n",
+ dprintf(vb.fd,"# [P] %d %08.f <%f,%f,%f>\n",
moldyn->count,moldyn->time,help/40.0,help/40.0,-0.8*help);
// atomic configuration
- for(i=0;i<moldyn->count;i++)
+ for(i=0;i<moldyn->count;i++) {
+ v3_sub(&strain,&(atom[i].r),&(atom[i].r_0));
+ check_per_bound(moldyn,&strain);
// atom type, positions, color and kinetic energy
dprintf(vb.fd,"%s %f %f %f %s %f\n",pse_name[atom[i].element],
atom[i].r.x,
atom[i].r.y,
atom[i].r.z,
pse_col[atom[i].element],
- atom[i].ekin);
+ //atom[i].ekin);
+ sqrt(v3_absolute_square(&strain)));
+ }
// bonds between atoms
+ #ifndef VISUAL_THREAD
process_2b_bonds(moldyn,&vb,visual_bonds_process);
+ #endif
// boundaries
if(dim.x) {
close(vb.fd);
+ #ifdef VISUAL_THREAD
+ pthread_exit(NULL);
+
+ }
+ #else
+
+ return 0;
+ }
+ #endif
+
+ /*
+ * fpu cntrol functions
+ */
+
+ // set rounding to double (eliminates -ffloat-store!)
+ int fpu_set_rtd(void) {
+
+ fpu_control_t ctrl;
+
+ _FPU_GETCW(ctrl);
+
+ ctrl&=~_FPU_EXTENDED;
+ ctrl|=_FPU_DOUBLE;
+
+ _FPU_SETCW(ctrl);
+
return 0;
}
u8 brand; /* brand id */
int tag; /* atom unique id (number of atom) */
u8 attr; /* attributes */
+ int pbc[3]; /* pb crossing in x, y and z direction */
} t_atom;
#define ATOM_ATTR_FP 0x01 /* fixed position (bulk material) */
#define DEFAULT_ATOM_ATTR 0x74 // 1,2,3 body interaction + visualize
+ /* special list structure for low mem approach */
+ typedef struct s_lowmem_list {
+ int *head;
+ int *list;
+ } t_lowmem_list;
+
/* cell lists */
typedef struct s_linkcell {
int nx,ny,nz; /* amount of cells in x, y and z direction */
double x,y,z; /* the actual cell lengthes */
#ifdef STATIC_LISTS
int **subcell; /* pointer to the cell lists */
+ #elif LOWMEM_LISTS
+ t_lowmem_list *subcell; /* low mem approach list */
#else
t_list *subcell; /* pointer to the cell lists */
#endif
double volume; /* volume of sim cell (dim.x*dim.y*dim.z) */
/* potential force function and parameter pointers */
- int (*func1b)(struct s_moldyn *moldyn,t_atom *ai);
- int (*func2b)(struct s_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc);
- int (*func3b_j1)(struct s_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc);
- int (*func3b_j2)(struct s_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc);
- int (*func3b_j3)(struct s_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc);
- int (*func3b_k1)(struct s_moldyn *moldyn,
- t_atom *ai,t_atom *aj,t_atom *ak,u8 bck);
- int (*func3b_k2)(struct s_moldyn *moldyn,
- t_atom *ai,t_atom *aj,t_atom *ak,u8 bck);
+ int (*func_i0)(struct s_moldyn *moldyn,t_atom *ai);
+ int (*func_j0)(struct s_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc);
+ int (*func_j0_k0)(struct s_moldyn *moldyn,
+ t_atom *ai,t_atom *aj,t_atom *ak,u8 bck);
+ int (*func_j0e)(struct s_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc);
+ int (*func_j1)(struct s_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc);
+ int (*func_j1_k0)(struct s_moldyn *moldyn,
+ t_atom *ai,t_atom *aj,t_atom *ak,u8 bck);
+ int (*func_j1c)(struct s_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc);
+ int (*func_j1_k1)(struct s_moldyn *moldyn,
+ t_atom *ai,t_atom *aj,t_atom *ak,u8 bck);
+ int (*func_j1e)(struct s_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc);
void *pot_params;
unsigned char run3bp;
double t_sum; /* sum over all t */
double t_avg; /* average value of t */
+ /* for sale! */
t_virial gvir; /* global virial (absolute coordinates) */
- double gv;
- double gv_sum;
- double gv_avg;
-
- double gp; /* pressure computed from global virial */
- double gp_sum; /* sum over all gp */
- double gp_avg; /* average value of gp */
+ //double gv;
+ //double gv_sum;
+ //double gv_avg;
+ double sale1;
+ double sale2;
+ double sale3;
+
+ // gp stuff exchanged by kinetic energies
+ //double gp; /* pressure computed from global virial */
+ //double gp_sum; /* sum over all gp */
+ //double gp_avg; /* average value of gp */
+ double ekinx;
+ double ekiny;
+ double ekinz;
t_virial vir; /* actual virial */
double virial;
int fd;
} t_vb;
+ typedef struct s_part_params {
+ u8 type;
+ double r;
+ t_3dvec p;
+ t_3dvec d;
+ } t_part_params;
+
+ #define PART_INSIDE_R 1
+ #define PART_OUTSIDE_R 2
+ #define PART_INSIDE_D 3
+ #define PART_OUTSIDE_D 4
+
+ typedef struct s_defect_params {
+ u8 type;
+ u8 stype;
+ double od;
+ double dd;
+ int element;
+ u8 brand;
+ u8 attr;
+ } t_defect_params;
+
+ #define DEFECT_TYPE_0D 1
+ #define DEFECT_TYPE_1D 2
+ #define DEFECT_TYPE_2D 3
+ #define DEFECT_TYPE_3D 4
+
+ #define DEFECT_STYPE_DB_X 1
+ #define DEFECT_STYPE_DB_Y 2
+ #define DEFECT_STYPE_DB_Z 3
+ #define DEFECT_STYPE_DB_R 4
+
+ typedef struct s_offset_params {
+ t_3dvec o;
+ u8 use;
+ } t_offset_params;
+
/*
*
* defines
#define MOLDYN_POTENTIAL_LJ 0x01
#define MOLDYN_POTENTIAL_TM 0x02
#define MOLDYN_POTENTIAL_AM 0x03
+#define MOLDYN_POTENTIAL_AO 0x04
#define LOG_TOTAL_ENERGY 0x01
#define LOG_TOTAL_MOMENTUM 0x02
#define FCC 0x02
#define DIAMOND 0x04
#define ZINCBLENDE 0x08
+ #define NONE 0x80
/*
* more includes
*/
- #include "pse.h"
+ //#include "pse.h"
/*
*
int moldyn_set_log(t_moldyn *moldyn,u8 type,int timer);
int moldyn_log_shutdown(t_moldyn *moldyn);
- int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass,
- u8 attr,u8 brand,int a,int b,int c,t_3dvec *origin);
- int add_atom(t_moldyn *moldyn,int element,double mass,u8 brand,u8 attr,
+ int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,
+ u8 attr,u8 brand,int a,int b,int c,t_3dvec *origin,
+ t_part_params *p_params,t_defect_params *d_params,
+ t_offset_params *o_params);
+ int add_atom(t_moldyn *moldyn,int element,u8 brand,u8 attr,
t_3dvec *r,t_3dvec *v);
int del_atom(t_moldyn *moldyn,int tag);
- int cubic_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin);
- int fcc_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin);
- int diamond_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin);
+ int cubic_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin,
+ t_part_params *p_params,t_defect_params *d_params);
+ int fcc_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin,
+ t_part_params *p_params,t_defect_params *d_params);
+ int diamond_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin,
+ t_part_params *p_params,t_defect_params *d_params);
int destroy_atoms(t_moldyn *moldyn);
int thermal_init(t_moldyn *moldyn,u8 equi_init);
int link_cell_update(t_moldyn *moldyn);
#ifdef STATIC_LISTS
int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,int **cell);
+ #elif LOWMEM_LISTS
+ int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,int *cell);
#else
int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,t_list *cell);
#endif
//inline int virial_calc(t_atom *a,t_3dvec *f,t_3dvec *d)
// __attribute__((always_inline));
int check_per_bound(t_moldyn *moldyn,t_3dvec *a);
+ int check_per_bound_and_care_for_pbc(t_moldyn *moldyn,t_atom *a);
//inline int check_per_bound(t_moldyn *moldyn,t_3dvec *a)
// __attribute__((always_inline));
int process_2b_bonds(t_moldyn *moldyn,void *data,
int (*process)(t_moldyn *moldyn,t_atom *itom,t_atom *jtom,
void *data,u8 bc));
+ int process_neighbours(t_moldyn *moldyn,void *data,t_atom *atom,
+ int (*process)(t_moldyn *moldyn,t_atom *atom,t_atom *natom,
+ void *data,u8 bc));
+
int get_line(int fd,char *line,int max);
int pair_correlation_init(t_moldyn *moldyn,double dr);
int calculate_diffusion_coefficient(t_moldyn *moldyn,double *dc);
+ int calculate_msd(t_moldyn *moldyn,double *msd);
int calculate_pair_correlation_process(t_moldyn *moldyn,t_atom *itom,
t_atom *jtom,void *data,u8 bc);
int calculate_pair_correlation(t_moldyn *moldyn,double dr,void *ptr);
int visual_init(t_moldyn *moldyn,char *filebase);
int visual_bonds_process(t_moldyn *moldyn,t_atom *itom,t_atom *jtom,
void *data,u8 bc);
+ #ifdef VISUAL_THREAD
+ void *visual_atoms(void *ptr);
+ #else
int visual_atoms(t_moldyn *moldyn);
+ #endif
+
+ int fpu_set_rtd(void);
#endif
p->mu[0]=ALBE_MU_SI;
p->gamma[0]=ALBE_GAMMA_SI;
p->c[0]=ALBE_C_SI;
+ p->c2[0]=p->c[0]*p->c[0];
p->d[0]=ALBE_D_SI;
+ p->d2[0]=p->d[0]*p->d[0];
+ p->c2d2[0]=p->c2[0]/p->d2[0];
p->h[0]=ALBE_H_SI;
switch(element2) {
case C:
p->mu[1]=ALBE_MU_C;
p->gamma[1]=ALBE_GAMMA_C;
p->c[1]=ALBE_C_C;
+ p->c2[1]=p->c[1]*p->c[1];
p->d[1]=ALBE_D_C;
+ p->d2[1]=p->d[1]*p->d[1];
+ p->c2d2[1]=p->c2[1]/p->d2[1];
p->h[1]=ALBE_H_C;
/* mixed type: silicon carbide */
p->Smixed=ALBE_S_SIC;
p->mu_m=ALBE_MU_SIC;
p->gamma_m=ALBE_GAMMA_SIC;
p->c_mixed=ALBE_C_SIC;
+ p->c2_mixed=p->c_mixed*p->c_mixed;
p->d_mixed=ALBE_D_SIC;
+ p->d2_mixed=p->d_mixed*p->d_mixed;
+ p->c2d2_m=p->c2_mixed/p->d2_mixed;
p->h_mixed=ALBE_H_SIC;
break;
default:
p->S2[0]=p->S[0]*p->S[0];
p->S2[1]=p->S[1]*p->S[1];
p->S2mixed=p->Smixed*p->Smixed;
+ p->c2[0]=p->c[0]*p->c[0];
+ p->c2[1]=p->c[1]*p->c[1];
+ p->c2_mixed=p->c_mixed*p->c_mixed;
+ p->d2[0]=p->d[0]*p->d[0];
+ p->d2[1]=p->d[1]*p->d[1];
+ p->d2_mixed=p->d_mixed*p->d_mixed;
+ p->c2d2[0]=p->c2[0]/p->d2[0];
+ p->c2d2[1]=p->c2[1]/p->d2[1];
+ p->c2d2_m=p->c2_mixed/p->d2_mixed;
printf("[albe] mult parameter info:\n");
printf(" S (A) | %f | %f | %f\n",p->S[0],p->S[1],p->Smixed);
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(" gamma | %f | %f\n",p->gamma[0],p->gamma[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(" gamma | %f | %f | %f\n",p->gamma[0],p->gamma[1],p->gamma_m);
+ printf(" c | %f | %f | %f\n",p->c[0],p->c[1],p->c_mixed);
+ printf(" d | %f | %f | %f\n",p->d[0],p->d[1],p->d_mixed);
+ printf(" c2 | %f | %f | %f\n",p->c2[0],p->c2[1],p->c2_mixed);
+ printf(" d2 | %f | %f | %f\n",p->d2[0],p->d2[1],p->d2_mixed);
+ printf(" c2d2 | %f | %f | %f\n",p->c2d2[0],p->c2d2[1],p->c2d2_m);
+ printf(" h | %f | %f | %f\n",p->h[0],p->h[1],p->h_mixed);
return 0;
}
-/* albe 3 body potential function (first ij loop) */
-int albe_mult_3bp_j1(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
+/* first i loop */
+int albe_mult_i0(t_moldyn *moldyn,t_atom *ai) {
t_albe_mult_params *params;
t_albe_exchange *exchange;
- unsigned char brand;
- double S2;
- t_3dvec dist_ij;
- double d_ij2,d_ij;
+
+ int i;
params=moldyn->pot_params;
exchange=&(params->exchange);
- /* reset zeta sum */
- exchange->zeta_ij=0.0;
+ /* zero exchange values */
+ memset(exchange->zeta,0,ALBE_MAXN*sizeof(double));
+ for(i=0;i<ALBE_MAXN;i++)
+ memset(exchange->dzeta[i],0,ALBE_MAXN*sizeof(t_3dvec));
+ exchange->jcnt=0;
+ exchange->j2cnt=0;
- /*
- * set ij depending values
- */
+ return 0;
+}
+/* first j loop within first i loop */
+int albe_mult_i0_j0(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
+
+ t_albe_mult_params *params;
+ t_albe_exchange *exchange;
+
+ double S2,S,R,d2,d,s_r,arg;
+ t_3dvec dist;
+ int j;
+ u8 brand;
+
+ params=moldyn->pot_params;
+ exchange=&(params->exchange);
+
+ /* get j counter */
+ j=exchange->jcnt;
+
+ /* set ij depending values */
brand=ai->brand;
if(brand==aj->brand) {
S2=params->S2[brand];
}
/* dist_ij, d_ij2 */
- v3_sub(&dist_ij,&(aj->r),&(ai->r));
- if(bc) check_per_bound(moldyn,&dist_ij);
- d_ij2=v3_absolute_square(&dist_ij);
+ v3_sub(&dist,&(aj->r),&(ai->r));
+ if(bc) check_per_bound(moldyn,&dist);
+ exchange->dist[j]=dist;
+ d2=v3_absolute_square(&dist);
+ exchange->d2[j]=d2;
/* if d_ij2 > S2 => no force & potential energy contribution */
- if(d_ij2>S2) {
+ if(d2>S2) {
moldyn->run3bp=0;
+ exchange->skip[j]=1;
+ exchange->jcnt+=1;
return 0;
}
+ exchange->skip[j]=0;
+
+ /* more ij depending values */
+ if(brand==aj->brand) {
+ R=params->R[brand];
+ S=params->S[brand];
+ /* albe needs i,(j/k) depending c,d,h and gamma values */
+ exchange->gamma_[j]=&(params->gamma[brand]);
+ exchange->c_[j]=&(params->c[brand]);
+ exchange->d_[j]=&(params->d[brand]);
+ exchange->h_[j]=&(params->h[brand]);
+ exchange->c2_[j]=&(params->c2[brand]);
+ exchange->d2_[j]=&(params->d2[brand]);
+ exchange->c2d2_[j]=&(params->c2d2[brand]);
+ }
+ else {
+ R=params->Rmixed;
+ S=params->Smixed;
+ /* albe needs i,(j/k) depending c,d,h and gamma values */
+ exchange->gamma_[j]=&(params->gamma_m);
+ exchange->c_[j]=&(params->c_mixed);
+ exchange->d_[j]=&(params->d_mixed);
+ exchange->h_[j]=&(params->h_mixed);
+ exchange->c2_[j]=&(params->c2_mixed);
+ exchange->d2_[j]=&(params->d2_mixed);
+ exchange->c2d2_[j]=&(params->c2d2_m);
+ }
/* d_ij */
- d_ij=sqrt(d_ij2);
+ d=sqrt(d2);
+ exchange->d[j]=d;
+
+ /* f_c, df_c */
+ if(d<R) {
+ exchange->f_c[j]=1.0;
+ exchange->df_c[j]=0.0;
+ }
+ else {
+ s_r=S-R;
+ arg=M_PI*(d-R)/s_r;
+ exchange->f_c[j]=0.5+0.5*cos(arg);
+ exchange->df_c[j]=0.5*sin(arg)*(M_PI/(s_r*d));
+ }
- /* store values */
- exchange->dist_ij=dist_ij;
- exchange->d_ij2=d_ij2;
- exchange->d_ij=d_ij;
+ /* reset k counter */
+ exchange->kcnt=0;
- /* reset k counter for first k loop */
- exchange->kcount=0;
-
return 0;
}
-/* albe 3 body potential function (first k loop) */
-int albe_mult_3bp_k1(t_moldyn *moldyn,
- t_atom *ai,t_atom *aj,t_atom *ak,u8 bc) {
+/* first k loop within first j loop within first i loop */
+int albe_mult_i0_j0_k0(t_moldyn *moldyn,
+ t_atom *ai,t_atom *aj,t_atom *ak,u8 bc) {
t_albe_mult_params *params;
t_albe_exchange *exchange;
- unsigned char brand;
- double R,S,S2;
- t_3dvec dist_ij,dist_ik;
- double d_ik2,d_ik,d_ij;
- double cos_theta,h_cos,d2_h_cos2,frac,g,dg,s_r,arg;
- double f_c_ik,df_c_ik;
- int kcount;
+
+ int j,k;
+ t_3dvec distj,distk;
+ double dj,dk,djdk_inv,cos_theta;
+ double gj,dgj,h_cos_j,d2_h_cos2_j,frac_j;
+ double gk,dgk,h_cos_k,d2_h_cos2_k,frac_k;
+ t_3dvec dcosdrj,dcosdrk,tmp;
+ t_3dvec *dzjj,*dzkk,*dzjk,*dzkj;
params=moldyn->pot_params;
exchange=&(params->exchange);
- kcount=exchange->kcount;
- if(kcount>ALBE_MAXN) {
- printf("FATAL: neighbours = %d\n",kcount);
- printf(" -> %d %d %d\n",ai->tag,aj->tag,ak->tag);
+ if(aj==ak) {
+ exchange->kcnt+=1;
+ return 0;
}
- /* ik constants */
- brand=ai->brand;
- if(brand==ak->brand) {
- R=params->R[brand];
- S=params->S[brand];
- S2=params->S2[brand];
- /* albe needs i,k depending c,d,h and gamma values */
- exchange->gamma_i=&(params->gamma[brand]);
- exchange->c_i=&(params->c[brand]);
- exchange->d_i=&(params->d[brand]);
- exchange->h_i=&(params->h[brand]);
- }
- else {
- R=params->Rmixed;
- S=params->Smixed;
- S2=params->S2mixed;
- /* albe needs i,k depending c,d,h and gamma values */
- exchange->gamma_i=&(params->gamma_m);
- exchange->c_i=&(params->c_mixed);
- exchange->d_i=&(params->d_mixed);
- exchange->h_i=&(params->h_mixed);
+ /* k<j & check whether to run k */
+ j=exchange->jcnt;
+ k=exchange->kcnt;
+ if(k>=ALBE_MAXN) {
+ printf("FATAL: too many neighbours! (%d)\n",k);
+ printf(" atom i:%d | j:%d | k:%d\n",ai->tag,aj->tag,ak->tag);
}
- exchange->ci2=*(exchange->c_i)**(exchange->c_i);
- exchange->di2=*(exchange->d_i)**(exchange->d_i);
- exchange->ci2di2=exchange->ci2/exchange->di2;
-
- /* dist_ik, d_ik2 */
- v3_sub(&dist_ik,&(ak->r),&(ai->r));
- if(bc) check_per_bound(moldyn,&dist_ik);
- d_ik2=v3_absolute_square(&dist_ik);
-
- /* store data for second k loop */
- exchange->dist_ik[kcount]=dist_ik;
- exchange->d_ik2[kcount]=d_ik2;
-
- /* return if not within cutoff */
- if(d_ik2>S2) {
- exchange->kcount++;
+ if((k>=j)|(exchange->skip[k])) {
+ exchange->kcnt+=1;
return 0;
}
- /* d_ik */
- d_ik=sqrt(d_ik2);
-
- /* dist_ij, d_ij */
- dist_ij=exchange->dist_ij;
- d_ij=exchange->d_ij;
+ /* distances */
+ distj=exchange->dist[j];
+ distk=exchange->dist[k];
+ dj=exchange->d[j];
+ dk=exchange->d[k];
+ djdk_inv=1.0/(dj*dk);
/* cos theta */
- cos_theta=v3_scalar_product(&dist_ij,&dist_ik)/(d_ij*d_ik);
-
- /* g_ijk */
- h_cos=*(exchange->h_i)+cos_theta; // + in albe formalism
- d2_h_cos2=exchange->di2+(h_cos*h_cos);
- frac=exchange->ci2/d2_h_cos2;
- g=*(exchange->gamma_i)*(1.0+exchange->ci2di2-frac);
- dg=2.0*frac**(exchange->gamma_i)*h_cos/d2_h_cos2; // + in albe f..
-
- /* zeta sum += f_c_ik * g_ijk */
- if(d_ik<=R) {
- exchange->zeta_ij+=g;
- f_c_ik=1.0;
- df_c_ik=0.0;
+ cos_theta=v3_scalar_product(&distj,&distk)*djdk_inv;
+
+ /* g(cos(theta)) ij and ik values */
+ h_cos_j=*(exchange->h_[j])+cos_theta; // + in albe formalism
+ d2_h_cos2_j=*exchange->d2_[j]+(h_cos_j*h_cos_j);
+ frac_j=*exchange->c2_[j]/d2_h_cos2_j;
+ gj=1.0+*exchange->c2d2_[j]-frac_j;
+ gj*=*(exchange->gamma_[j]);
+ dgj=*(exchange->gamma_[j])*2.0*frac_j*h_cos_j/d2_h_cos2_j; // + in albe
+ if(ak->brand==aj->brand) {
+ gk=gj;
+ dgk=dgj;
}
else {
- s_r=S-R;
- arg=M_PI*(d_ik-R)/s_r;
- f_c_ik=0.5+0.5*cos(arg);
- df_c_ik=0.5*sin(arg)*(M_PI/(s_r*d_ik));
- exchange->zeta_ij+=f_c_ik*g;
+ h_cos_k=*(exchange->h_[k])+cos_theta;
+ d2_h_cos2_k=*exchange->d2_[k]+(h_cos_k*h_cos_k);
+ frac_k=*exchange->c2_[k]/d2_h_cos2_k;
+ gk=1.0+*exchange->c2d2_[k]-frac_k;
+ gk*=*(exchange->gamma_[k]);
+ dgk=*(exchange->gamma_[k])*2.0*frac_k*h_cos_k/d2_h_cos2_k;
}
- /* zeta - for albe: ik depending g function */
- //if(ai->tag==0) {
- // printf("------> %.15f %.15f\n",dj,dk);
- // printf("------> %.15f %.15f\n",dj,dk);
- //}
-
- exchange->zeta[j]+=(exchange->f_c[k]*gk);
- exchange->zeta[k]+=(exchange->f_c[j]*gj);
-
- /* cos theta derivatives */
- v3_scale(&dcosdrj,&distk,djdk_inv); // j
- v3_scale(&tmp,&distj,-cos_theta/exchange->d2[j]);
- v3_add(&dcosdrj,&dcosdrj,&tmp);
- v3_scale(&dcosdrk,&distj,djdk_inv); // k
- v3_scale(&tmp,&distk,-cos_theta/exchange->d2[k]);
- v3_add(&dcosdrk,&dcosdrk,&tmp);
+ #ifdef DEBUG
+ if(ai==&(moldyn->atom[DATOM]))
+ printf("zeta_ij: %f %f %f %f\n",f_c_ik*g,f_c_ik,g,d_ik);
+ #endif
- /* zeta derivatives */
- dzjj=&(exchange->dzeta[j][j]);
- dzkk=&(exchange->dzeta[k][k]);
- dzjk=&(exchange->dzeta[j][k]);
- dzkj=&(exchange->dzeta[k][j]);
- v3_scale(&tmp,&dcosdrj,exchange->f_c[k]*dgk);
- v3_add(dzjj,dzjj,&tmp); // j j
- v3_scale(&tmp,&dcosdrk,exchange->f_c[j]*dgj);
- v3_add(dzkk,dzkk,&tmp); // k k
- v3_scale(&tmp,&distk,-exchange->df_c[k]*gk); // dk rik = - di rik
- v3_add(dzjk,dzjk,&tmp);
- v3_scale(&tmp,&dcosdrk,exchange->f_c[k]*dgk);
- v3_add(dzjk,dzjk,&tmp); // j k
- v3_scale(&tmp,&distj,-exchange->df_c[j]*gj); // dj rij = - di rij
- v3_add(dzkj,dzkj,&tmp);
- v3_scale(&tmp,&dcosdrj,exchange->f_c[j]*dgj);
- v3_add(dzkj,dzkj,&tmp); // k j
+ /* store even more data for second k loop */
+ exchange->g[kcount]=g;
+ exchange->dg[kcount]=dg;
+ exchange->d_ik[kcount]=d_ik;
+ exchange->cos_theta[kcount]=cos_theta;
+ exchange->f_c_ik[kcount]=f_c_ik;
+ exchange->df_c_ik[kcount]=df_c_ik;
/* increase k counter */
- exchange->kcount++;
+ exchange->kcnt+=1;
+
+ return 0;
+}
+
+/* first j loop within first i loop */
+int albe_mult_i0_j1(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
+
+ t_albe_mult_params *params;
+ t_albe_exchange *exchange;
+
+ params=moldyn->pot_params;
+ exchange=&(params->exchange);
+
+ /* increase j counter */
+ exchange->jcnt+=1;
return 0;
}
-int albe_mult_3bp_j2(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
+/* second j loop within first i loop */
+int albe_mult_i0_j2(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
t_albe_mult_params *params;
t_albe_exchange *exchange;
- t_3dvec force;
- double f_a,df_a,b,db,f_c,df_c;
- double f_r,df_r;
- double scale;
- double mu,B;
- double lambda,A;
- double d_ij,r0;
- unsigned char brand;
- double S,R,s_r,arg;
+
+ int j;
+ double d,f_a,df_a,f_r,df_r,f_c,df_c,b,db;
+ double A,B,mu,lambda,r0;
double energy;
+ t_3dvec *dist,force;
+ double scale;
+ u8 brand;
params=moldyn->pot_params;
exchange=&(params->exchange);
+ /* get j counter */
+ j=exchange->j2cnt;
+
+ /* skip if j not within cutoff */
+ if(exchange->skip[j]) {
+ moldyn->run3bp=0;
+ exchange->j2cnt+=1;
+ return 0;
+ }
+
+ /* distance */
+ d=exchange->d[j];
+ dist=&(exchange->dist[j]);
+ f_c=exchange->f_c[j];
+ df_c=exchange->df_c[j];
+
+ /* determine parameters to calculate fa, dfa, fr, dfr */
brand=aj->brand;
if(brand==ai->brand) {
- S=params->S[brand];
- R=params->R[brand];
B=params->B[brand];
A=params->A[brand];
r0=params->r0[brand];
lambda=params->lambda[brand];
}
else {
- S=params->Smixed;
- R=params->Rmixed;
B=params->Bmixed;
A=params->Amixed;
r0=params->r0_mixed;
lambda=params->lambda_m;
}
- d_ij=exchange->d_ij;
-
- /* f_c, df_c */
- if(d_ij<R) {
- f_c=1.0;
- df_c=0.0;
- }
- 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));
- }
-
/* f_a, df_a */
- f_a=-B*exp(-mu*(d_ij-r0));
- df_a=mu*f_a/d_ij;
+ f_a=-B*exp(-mu*(d-r0));
+ df_a=mu*f_a/d;
/* f_r, df_r */
- f_r=A*exp(-lambda*(d_ij-r0));
- df_r=lambda*f_r/d_ij;
+ f_r=A*exp(-lambda*(d-r0));
+ df_r=lambda*f_r/d;
/* b, db */
- if(exchange->zeta_ij==0.0) {
- b=1.0;
- db=0.0;
- }
- else {
- b=1.0/sqrt(1.0+exchange->zeta_ij);
- db=-0.5*b/(1.0+exchange->zeta_ij);
- }
+ b=1.0/sqrt(1.0+exchange->zeta[j]);
+ db=-0.5*b/(1.0+exchange->zeta[j]);
+
+ /* energy contribution */
+ energy=0.5*f_c*(f_r-b*f_a); // - in albe formalism
+ moldyn->energy+=energy;
+ ai->e+=energy;
- /* force contribution for atom i */
+ /* force contribution for atom i due to ij bond */
scale=-0.5*(f_c*(df_r-b*df_a)+df_c*(f_r-b*f_a)); // - in albe formalism
- v3_scale(&force,&(exchange->dist_ij),scale);
+ v3_scale(&force,dist,scale);
v3_add(&(ai->f),&(ai->f),&force);
- /* force contribution for atom j */
+#ifdef NDEBUG
+if(ai->tag==0) {
+printf("force: %.15f %.15f %.15f | %d %d (ij) %.15f\n",force.x,force.y,force.z,ai->tag,aj->tag,exchange->zeta[j]);
+printf(" t: %.15f %.15f %.15f\n",ai->f.x,ai->f.y,ai->f.z);
+}
+#endif
+
+ /* force contribution for atom j due to ij bond */
v3_scale(&force,&force,-1.0); // dri rij = - drj rij
v3_add(&(aj->f),&(aj->f),&force);
- #ifdef NDEBUG
- if(aj->tag==0) {
- printf("force: %.15f %.15f %.15f | %d %d (ji) %.15f\n",force.x,force.y,force.z,aj->tag,ai->tag,exchange->zeta[j]);
- printf(" t: %.15f %.15f %.15f\n",aj->f.x,aj->f.y,aj->f.z);
- }
+ /* virial */
+ virial_calc(ai,&force,&(exchange->dist_ij));
+
+ #ifdef DEBUG
+ if((ai==&(moldyn->atom[DATOM]))|(aj==&(moldyn->atom[DATOM]))) {
+ printf("force 3bp (j2): [%d %d sum]\n",ai->tag,aj->tag);
+ printf(" adding %f %f %f\n",force.x,force.y,force.z);
+ if(ai==&(moldyn->atom[DATOM]))
+ printf(" total i: %f %f %f\n",ai->f.x,ai->f.y,ai->f.z);
+ if(aj==&(moldyn->atom[DATOM]))
+ printf(" total j: %f %f %f\n",aj->f.x,aj->f.y,aj->f.z);
+ printf(" energy: %f = %f %f %f %f\n",0.5*f_c*(b*f_a+f_r),
+ f_c,b,f_a,f_r);
+ printf(" %f %f %f\n",exchange->zeta_ij,.0,.0);
+ }
#endif
+ /* virial */
+ virial_calc(ai,&force,dist);
+
/* dzeta prefactor = - f_c f_a db, (* -0.5 due to force calc) */
exchange->pre_dzeta=0.5*f_a*f_c*db;
- /* energy contribution */
- energy=0.5*f_c*(f_r-b*f_a); // - in albe formalism
- moldyn->energy+=energy;
- ai->e+=energy;
+ /* force contribution (drj derivative) */
+ v3_scale(&force,&(exchange->dzeta[j][j]),exchange->pre_dzeta);
+ v3_add(&(aj->f),&(aj->f),&force);
+
+#ifdef NDEBUG
+if(aj->tag==0) {
+printf("force: %.15f %.15f %.15f | %d %d (j der)\n",force.x,force.y,force.z,aj->tag,ai->tag);
+printf(" t: %.15f %.15f %.15f\n",aj->f.x,aj->f.y,aj->f.z);
+}
+#endif
+
+ /* virial */
+ virial_calc(ai,&force,dist);
+
+ v3_scale(&force,&force,-1.0);
+ v3_add(&(ai->f),&(ai->f),&force);
+
+#ifdef NDEBUG
+if(ai->tag==0) {
+printf("force: %.15f %.15f %.15f | %d %d (i contr j der)\n",force.x,force.y,force.z,ai->tag,aj->tag);
+printf(" t: %.15f %.15f %.15f\n",ai->f.x,ai->f.y,ai->f.z);
+}
+#endif
/* reset k counter for second k loop */
- exchange->kcount=0;
+ exchange->kcnt=0;
return 0;
}
-/* albe 3 body potential function (second k loop) */
-int albe_mult_3bp_k2(t_moldyn *moldyn,
- t_atom *ai,t_atom *aj,t_atom *ak,u8 bc) {
+/* second k loop within second j loop within first i loop */
+int albe_mult_i0_j2_k0(t_moldyn *moldyn,
+ t_atom *ai,t_atom *aj,t_atom *ak,u8 bc) {
t_albe_mult_params *params;
t_albe_exchange *exchange;
- int kcount;
- t_3dvec dist_ik,dist_ij;
- double d_ik2,d_ik,d_ij2,d_ij;
- unsigned char brand;
- double S2;
- double g,dg,cos_theta;
- double pre_dzeta;
- double f_c_ik,df_c_ik;
- double dijdik_inv,fcdg,dfcg;
- t_3dvec dcosdrj,dcosdrk;
- t_3dvec force,tmp;
+
+ int j,k;
+ t_3dvec force;
params=moldyn->pot_params;
exchange=&(params->exchange);
- kcount=exchange->kcount;
-
- if(kcount>ALBE_MAXN)
- printf("FATAL: neighbours!\n");
-
- /* d_ik2 */
- d_ik2=exchange->d_ik2[kcount];
- brand=ak->brand;
- if(brand==ai->brand)
- S2=params->S2[brand];
- else
- S2=params->S2mixed;
-
- /* return if d_ik > S */
- if(d_ik2>S2) {
- exchange->kcount++;
+ if(aj==ak) {
+ exchange->kcnt+=1;
return 0;
}
- /* k!=j & check whether to run k */
- k=exchange->kcnt;
- j=exchange->j2cnt;
- if((k==j)|(exchange->skip[k])) {
- exchange->kcnt+=1;
- return 0;
- }
-
- /* force contribution (drk derivative) */
- v3_scale(&force,&(exchange->dzeta[j][k]),exchange->pre_dzeta);
- v3_add(&(ak->f),&(ak->f),&force);
+ /* prefactor dzeta */
+ pre_dzeta=exchange->pre_dzeta;
- #ifdef NDEBUG
- if(ak->tag==0) {
- printf("force: %.15f %.15f %.15f | %d %d %d (k der)\n",force.x,force.y,force.z,ai->tag,aj->tag,ak->tag);
- printf(" t: %.15f %.15f %.15f\n",ak->f.x,ak->f.y,ak->f.z);
- }
+ /* dist_ik, d_ik */
+ dist_ik=exchange->dist_ik[kcount];
+ d_ik=exchange->d_ik[kcount];
+
+ /* f_c_ik, df_c_ik */
+ f_c_ik=exchange->f_c_ik[kcount];
+ df_c_ik=exchange->df_c_ik[kcount];
+
+ /* dist_ij, d_ij2, d_ij */
+ dist_ij=exchange->dist_ij;
+ d_ij2=exchange->d_ij2;
+ d_ij=exchange->d_ij;
+
+ /* g, dg, cos_theta */
+ g=exchange->g[kcount];
+ dg=exchange->dg[kcount];
+ cos_theta=exchange->cos_theta[kcount];
+
+ /* cos_theta derivatives wrt j,k */
+ dijdik_inv=1.0/(d_ij*d_ik);
+ v3_scale(&dcosdrj,&dist_ik,dijdik_inv); // j
+ v3_scale(&tmp,&dist_ij,-cos_theta/d_ij2);
+ v3_add(&dcosdrj,&dcosdrj,&tmp);
+ v3_scale(&dcosdrk,&dist_ij,dijdik_inv); // k
+ v3_scale(&tmp,&dist_ik,-cos_theta/d_ik2);
+ v3_add(&dcosdrk,&dcosdrk,&tmp);
+
+ /* f_c_ik * dg, df_c_ik * g */
+ fcdg=f_c_ik*dg;
+ dfcg=df_c_ik*g;
+
+ /* derivative wrt j */
+ v3_scale(&force,&dcosdrj,fcdg*pre_dzeta);
+
+ /* force contribution */
+ v3_add(&(aj->f),&(aj->f),&force);
+
+ #ifdef DEBUG
+ if(aj==&(moldyn->atom[DATOM])) {
+ printf("force 3bp (k2): [%d %d %d]\n",ai->tag,aj->tag,ak->tag);
+ printf(" adding %f %f %f\n",force.x,force.y,force.z);
+ printf(" total j: %f %f %f\n",aj->f.x,aj->f.y,aj->f.z);
+ printf(" angle: %f\n",acos(cos_theta)*360.0/(2*M_PI));
+ printf(" d ij ik = %f %f\n",d_ij,d_ik);
+ }
#endif
/* virial */
- virial_calc(ai,&force,&(exchange->dist[k]));
+ virial_calc(ai,&force,&dist_ij);
+ /* force contribution to atom i */
v3_scale(&force,&force,-1.0);
v3_add(&(ai->f),&(ai->f),&force);
- #ifdef NDEBUG
- if(ai->tag==0) {
- printf("force: %.15f %.15f %.15f | %d %d %d -- %d(i contr k der)\n",force.x,force.y,force.z,ai->tag,aj->tag,ak->tag,k);
- printf(" t: %.15f %.15f %.15f\n",ai->f.x,ai->f.y,ai->f.z);
- printf(" ## %f\n",exchange->d[k]);
- }
+ /* derivative wrt k */
+ v3_scale(&force,&dist_ik,-1.0*dfcg); // dri rik = - drk rik
+ v3_scale(&tmp,&dcosdrk,fcdg);
+ v3_add(&force,&force,&tmp);
+ v3_scale(&force,&force,pre_dzeta);
+
- /* force contribution */
- v3_add(&(ak->f),&(ak->f),&force);
++ v3_scale(&force,&force,-1.0);
++ v3_add(&(ai->f),&(ai->f),&force);
+
+ #ifdef DEBUG
+ if(ak==&(moldyn->atom[DATOM])) {
+ printf("force 3bp (k2): [%d %d %d]\n",ai->tag,aj->tag,ak->tag);
+ printf(" adding %f %f %f\n",force.x,force.y,force.z);
+ printf(" total k: %f %f %f\n",ak->f.x,ak->f.y,ak->f.z);
+ printf(" angle: %f\n",acos(cos_theta)*360.0/(2*M_PI));
+ printf(" d ij ik = %f %f\n",d_ij,d_ik);
+ }
#endif
+ /* virial */
+ virial_calc(ai,&force,&dist_ik);
+
+ /* force contribution to atom i */
+ v3_scale(&force,&force,-1.0);
+ v3_add(&(ai->f),&(ai->f),&force);
+
/* increase k counter */
- exchange->kcount++;
+ exchange->kcnt+=1;
return 0;
+}
+
+int albe_mult_i0_j3(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
+ t_albe_mult_params *params;
+ t_albe_exchange *exchange;
+
+ params=moldyn->pot_params;
+ exchange=&(params->exchange);
+
+ /* increase j counter */
+ exchange->j2cnt+=1;
+
+ return 0;
}
int albe_mult_check_2b_bond(t_moldyn *moldyn,t_atom *itom,t_atom *jtom,u8 bc) {
#ifndef ALBE_H
#define ALBE_H
-#define ALBE_MAXN 16*27
+#define ALBE_MAXN (4*27)
/* albe exchange type */
typedef struct s_albe_exchange {
- t_3dvec dist_ij;
- double d_ij2;
- double d_ij;
+ t_3dvec dist[ALBE_MAXN];
+ double d2[ALBE_MAXN];
+ double d[ALBE_MAXN];
- t_3dvec dist_ik[ALBE_MAXN];
- double d_ik2[ALBE_MAXN];
- double d_ik[ALBE_MAXN];
+ double f_c[ALBE_MAXN];
+ double df_c[ALBE_MAXN];
- double f_c_ik[ALBE_MAXN];
- double df_c_ik[ALBE_MAXN];
+ double zeta[ALBE_MAXN];
+ t_3dvec dzeta[ALBE_MAXN][ALBE_MAXN];
- double g[ALBE_MAXN];
- double dg[ALBE_MAXN];
- double cos_theta[ALBE_MAXN];
+ u8 skip[ALBE_MAXN];
- double *gamma_i;
- double *c_i;
- double *d_i;
- double *h_i;
+ double *gamma_[ALBE_MAXN];
+ double *c_[ALBE_MAXN];
+ double *d_[ALBE_MAXN];
+ double *c2_[ALBE_MAXN];
+ double *d2_[ALBE_MAXN];
+ double *c2d2_[ALBE_MAXN];
+ double *h_[ALBE_MAXN];
- double ci2;
- double di2;
- double ci2di2;
-
- double zeta_ij;
double pre_dzeta;
- int kcount;
+ int jcnt;
+ int j2cnt;
+ int kcnt;
} t_albe_exchange;
/* albe mult (2!) potential parameters */
double gamma[2];
double gamma_m;
double c[2];
+ double c2[2];
double c_mixed;
+ double c2[2];
double c2_mixed;
double d[2];
+ double d2[2];
double d_mixed;
+ double d2[2];
double d2_mixed;
- double c2d2[2];
- double c2d2_m;
double h[2];
double h_mixed;
+ double c2d2[2];
+ double c2d2_m;
t_albe_exchange exchange; /* exchange between 2bp and 3bp calc */
} t_albe_mult_params;
/* function prototypes */
int albe_mult_set_params(t_moldyn *moldyn,int element1,int elemnt2);
- int albe_mult_i0(t_moldyn *moldyn,t_atom *ai);
- int albe_mult_i0_j0(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc);
- int albe_mult_i0_j0_k0(t_moldyn *moldyn,
- t_atom *ai,t_atom *aj,t_atom *ak,u8 bc);
- int albe_mult_i0_j1(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc);
- int albe_mult_i0_j2(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc);
- int albe_mult_i0_j2_k0(t_moldyn *moldyn,
- t_atom *ai,t_atom *aj,t_atom *ak,u8 bc);
- int albe_mult_i0_j3(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc);
+ int albe_mult_3bp_j1(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc);
+ int albe_mult_3bp_k1(t_moldyn *moldyn,
+ t_atom *ai,t_atom *aj,t_atom *ak,u8 bc);
+ int albe_mult_3bp_j2(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc);
+ int albe_mult_3bp_k2(t_moldyn *moldyn,
+ t_atom *ai,t_atom *aj,t_atom *ak,u8 bc);
int albe_mult_check_2b_bond(t_moldyn *moldyn,t_atom *itom,t_atom *jtom,u8 bc);
+ /* fast */
+ int albe_potential_force_calc(t_moldyn *moldyn);
/* albe potential parameter defines */
#define ALBE_MU_SI (1.4761*sqrt(2.0/1.842))
#define ALBE_GAMMA_SI 0.114354
#define ALBE_C_SI 2.00494
- #define ALBE_D_SI 0.81472
+ #define ALBE_D_SI 0.814719
#define ALBE_H_SI 0.259
#define ALBE_LC_SI 5.429
// carbon
#define ALBE_R_C (2.00-0.15)
#define ALBE_S_C (2.00+0.15)
- #define ALBE_A_C (6.00*EV/1.167)
- #define ALBE_B_C (-2.167*6.00*EV/1.167)
- #define ALBE_R0_C 1.4276
- #define ALBE_LAMBDA_C (2.0099*sqrt(2.0*2.167))
- #define ALBE_MU_C (2.0099*sqrt(2.0/2.167))
- #define ALBE_GAMMA_C 0.11233
- #define ALBE_C_C 181.910
- #define ALBE_D_C 6.28433
- #define ALBE_H_C 0.5556
+ #define ALBE_A_C (6.00*EV/1.1671419)
+ #define ALBE_B_C (-2.1671419*6.00*EV/1.1671419)
+ #define ALBE_R0_C 1.4276442
+ #define ALBE_LAMBDA_C (2.0099457*sqrt(2.0*2.1671419))
+ #define ALBE_MU_C (2.0099457*sqrt(2.0/2.1671419))
+ #define ALBE_GAMMA_C 0.1123327
+ #define ALBE_C_C 181.9100526
+ #define ALBE_D_C 6.2843249
+ #define ALBE_H_C 0.5556181
#define ALBE_LC_C 3.566
// mixed: silicon carbide
#define ALBE_R_SIC (2.40-0.20)
#define ALBE_S_SIC (2.40+0.20)
- #define ALBE_A_SIC (4.36*EV/0.847)
- #define ALBE_B_SIC (-1.847*4.36*EV/0.847)
+ #define ALBE_A_SIC (4.36*EV/0.8474739)
+ #define ALBE_B_SIC (-1.8474739*4.36*EV/0.8474739)
#define ALBE_R0_SIC 1.79
- #define ALBE_LAMBDA_SIC (1.6991*sqrt(2.0*1.847))
- #define ALBE_MU_SIC (1.6991*sqrt(2.0/1.847))
- #define ALBE_GAMMA_SIC 0.011877
- #define ALBE_C_SIC 273987
- #define ALBE_D_SIC 180.314
+ #define ALBE_LAMBDA_SIC (1.6990751*sqrt(2.0*1.8474739))
+ #define ALBE_MU_SIC (1.6990751*sqrt(2.0/1.8474739))
+ #define ALBE_GAMMA_SIC 0.0118769
+ #define ALBE_C_SIC 273986.61
+ #define ALBE_D_SIC 180.31411
#define ALBE_H_SIC 0.68
#define ALBE_LC_SIC 4.359
projects / physik / posic.git / commitdiff