#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
return 0;
}
+int del_stages(t_mdrun *mdrun) {
+
+ t_list *sl;
+ t_stage *stage;
+
+ sl=&(mdrun->stage);
+
+ list_reset_f(sl);
+
+ if(sl->start==NULL)
+ return 0;
+
+ do {
+ stage=sl->current->data;
+ free(stage->params);
+ free(stage);
+ } while(list_next_f(sl)!=L_NO_NEXT_ELEMENT);
+
+ return 0;
+}
+
+int add_stage(t_mdrun *mdrun,u8 type,void *params) {
+
+ int psize;
+
+ t_stage *stage;
+
+ switch(type) {
+ case STAGE_DISPLACE_ATOM:
+ psize=sizeof(t_displace_atom_params);
+ break;
+ case STAGE_INSERT_ATOMS:
+ psize=sizeof(t_insert_atoms_params);
+ break;
+ case STAGE_CONTINUE:
+ psize=sizeof(t_continue_params);
+ break;
+ case STAGE_ANNEAL:
+ psize=sizeof(t_anneal_params);
+ break;
+ case STAGE_CHAATTR:
+ psize=sizeof(t_chaattr_params);
+ break;
+ case STAGE_CHSATTR:
+ psize=sizeof(t_chsattr_params);
+ break;
+ default:
+ printf("%s unknown stage type: %02x\n",ME,type);
+ return -1;
+ }
+
+ stage=malloc(sizeof(t_stage));
+ if(stage==NULL) {
+ perror("[mdrun] malloc (add stage)");
+ return -1;
+ }
+
+ stage->type=type;
+ stage->executed=FALSE;
+
+ stage->params=malloc(psize);
+ if(stage->params==NULL) {
+ perror("[mdrun] malloc (stage params)");
+ return -1;
+ }
+
+ memcpy(stage->params,params,psize);
+
+ list_add_immediate_f(&(mdrun->stage),stage);
+
+ return 0;
+}
+
int mdrun_parse_config(t_mdrun *mdrun) {
int fd,ret;
char error[128];
char line[128];
char *wptr;
- char word[16][32];
+ char word[16][64];
int wcnt;
+ int i,o;
+
+ t_displace_atom_params dap;
+ t_insert_atoms_params iap;
+ t_continue_params cp;
+ t_anneal_params ap;
+ t_chaattr_params cap;
+ t_chsattr_params csp;
/* open config file */
fd=open(mdrun->cfile,O_RDONLY);
if((line[0]=='#')|(ret==1))
continue;
+ // reset
+ memset(&iap,0,sizeof(t_insert_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));
+
// get command + args
wcnt=0;
while(1) {
wptr=strtok(line," \t");
if(wptr==NULL)
break;
- strncpy(word[wcnt],wptr,32);
+ strncpy(word[wcnt],wptr,64);
wcnt+=1;
}
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))
if(!strncmp(word[1],"lj",2))
mdrun->potential=MOLDYN_POTENTIAL_LJ;
}
+ else if(!strncmp(word[0],"continue",8))
+ strncpy(mdrun->continue_file,word[1],128);
else if(!strncmp(word[0],"cutoff",6))
mdrun->cutoff=atof(word[1]);
+ else if(!strncmp(word[0],"nnd",3))
+ mdrun->nnd=atof(word[1]);
else if(!strncmp(word[0],"intalgo",7)) {
if(!strncmp(word[1],"verlet",5))
mdrun->intalgo=MOLDYN_INTEGRATE_VERLET;
}
else if(!strncmp(word[0],"element1",8)) {
mdrun->element1=atoi(word[1]);
- switch(mdrun->element1) {
- case SI:
- mdrun->m1=M_SI;
- break;
- case C:
- mdrun->m1=M_C;
- break;
- default:
- printf("%s unknown element1: %s|%d\n",
- ME,word[1],mdrun->element1);
- return -1;
- }
+ mdrun->m1=pse_mass[mdrun->element1];
}
else if(!strncmp(word[0],"element2",8)) {
mdrun->element2=atoi(word[1]);
- switch(mdrun->element2) {
- case SI:
- mdrun->m2=M_SI;
- break;
- case C:
- mdrun->m2=M_C;
- break;
- default:
- printf("%s unknown element2: %s|%d\n",
- ME,word[1],mdrun->element2);
- return -1;
- }
+ mdrun->m2=pse_mass[mdrun->element2];
}
- else if(!strncmp(word[0],"filllc",6)) {
- mdrun->lx=atoi(word[1]);
- mdrun->ly=atoi(word[2]);
- mdrun->lz=atoi(word[3]);
+ 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]);
}
- else if(!strncmp(word[0],"aattrib",7)) {
+ else if(!strncmp(word[0],"aattr",5)) {
// for aatrib line we need a special stage
// containing one schedule of 0 loops ...
- printf("%s aattrib: %s\n",ME,word[1]);
+ for(i=0;i<strlen(word[1]);i++) {
+ switch(word[1][i]) {
+ case 't':
+ cap.type|=CHAATTR_TOTALV;
+ break;
+ case 'r':
+ cap.type|=CHAATTR_REGION;
+ break;
+ case 'e':
+ cap.type|=CHAATTR_ELEMENT;
+ break;
+ 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]);
+ i+=6;
+ }
+ if(cap.type&CHAATTR_ELEMENT) {
+ cap.element=atoi(word[i]);
+ i+=1;
+ }
+ for(o=0;o<strlen(word[i]);o++) {
+ switch(word[i][o]) {
+ case 'b':
+ cap.attr|=ATOM_ATTR_VB;
+ break;
+ case 'h':
+ cap.attr|=ATOM_ATTR_HB;
+ break;
+ case 'v':
+ cap.attr|=ATOM_ATTR_VA;
+ break;
+ case 'f':
+ cap.attr|=ATOM_ATTR_FP;
+ break;
+ case '1':
+ cap.attr|=ATOM_ATTR_1BP;
+ break;
+ case '2':
+ cap.attr|=ATOM_ATTR_2BP;
+ break;
+ case '3':
+ cap.attr|=ATOM_ATTR_3BP;
+ break;
+ default:
+ break;
+ }
+ }
+ add_stage(mdrun,STAGE_CHAATTR,&cap);
}
- else if(!strncmp(word[0],"eattrib",7)) {
- mdrun->p_tau=atof(word[1]);
- mdrun->t_tau=atof(word[2]);
+ else if(!strncmp(word[0],"sattr",5)) {
+ // for satrib line we need a special stage
+ // containing one schedule of 0 loops ...
+ csp.type=0;
+ for(i=1;i<wcnt;i++) {
+ if(!strncmp(word[i],"pctrl",5)) {
+ csp.ptau=0.01/(atof(word[++i])*GPA);
+ csp.type|=CHSATTR_PCTRL;
+ }
+ if(!strncmp(word[i],"tctrl",5)) {
+ csp.ttau=atof(word[++i]);
+ csp.type|=CHSATTR_TCTRL;
+ }
+ if(!strncmp(word[i],"prelax",6)) {
+ csp.dp=atof(word[++i])*BAR;
+ csp.type|=CHSATTR_PRELAX;
+ }
+ if(!strncmp(word[i],"trelax",6)) {
+ csp.dt=atof(word[++i]);
+ csp.type|=CHSATTR_TRELAX;
+ }
+ if(!strncmp(word[i],"rsteps",6)) {
+ csp.rsteps=atoi(word[++i]);
+ csp.type|=CHSATTR_RSTEPS;
+ }
+ if(!strncmp(word[i],"avgrst",6)) {
+ csp.avgrst=atoi(word[++i]);
+ csp.type|=CHSATTR_AVGRST;
+ }
+ }
+ add_stage(mdrun,STAGE_CHSATTR,&csp);
}
else if(!strncmp(word[0],"prerun",6))
mdrun->prerun=atoi(word[1]);
mdrun->visualize=atoi(word[1]);
else if(!strncmp(word[0],"stage",5)) {
// for every stage line, add a stage
- printf("%s stage: %s\n",ME,word[1]);
+ if(!strncmp(word[1],"displace",8)) {
+ dap.nr=atoi(word[2]);
+ dap.dx=atof(word[3]);
+ dap.dy=atof(word[4]);
+ dap.dz=atof(word[5]);
+ add_stage(mdrun,STAGE_DISPLACE_ATOM,&dap);
+ }
+ else if(!strncmp(word[1],"ins_atoms",9)) {
+ iap.ins_steps=atoi(word[2]);
+ iap.ins_atoms=atoi(word[3]);
+ iap.element=atoi(word[4]);
+ iap.brand=atoi(word[5]);
+ for(i=0;i<strlen(word[6]);i++) {
+ switch(word[6][i]) {
+ case 'b':
+ iap.attr|=ATOM_ATTR_VB;
+ break;
+ case 'h':
+ iap.attr|=ATOM_ATTR_HB;
+ break;
+ case 'v':
+ iap.attr|=ATOM_ATTR_VA;
+ break;
+ case 'f':
+ iap.attr|=ATOM_ATTR_FP;
+ break;
+ case '1':
+ iap.attr|=ATOM_ATTR_1BP;
+ break;
+ case '2':
+ iap.attr|=ATOM_ATTR_2BP;
+ break;
+ case '3':
+ iap.attr|=ATOM_ATTR_3BP;
+ break;
+ default:
+ break;
+ }
+ }
+ switch(word[7][0]) {
+ // insertion types
+ case 'p':
+ iap.type=INS_POS;
+ iap.x0=atof(word[8]);
+ iap.y0=atof(word[9]);
+ iap.z0=atof(word[10]);
+ break;
+ case 'r':
+ if(word[8][0]=='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]);
+ }
+ default:
+ break;
+ }
+ add_stage(mdrun,STAGE_INSERT_ATOMS,&iap);
+ }
+ else if(!strncmp(word[1],"continue",8)) {
+ cp.runs=atoi(word[2]);
+ add_stage(mdrun,STAGE_CONTINUE,&cp);
+ }
+ else if(!strncmp(word[1],"anneal",6)) {
+ ap.count=0;
+ ap.runs=atoi(word[2]);
+ ap.dt=atof(word[3]);
+ add_stage(mdrun,STAGE_ANNEAL,&ap);
+ }
+ else {
+ printf("%s unknown stage type: %s\n",
+ ME,word[1]);
+ return -1;
+ }
}
else {
- printf("%s unknown command %s, skipped!\n",ME,wptr);
+ printf("%s unknown keyword '%s', skipped!\n",
+ ME,word[0]);
continue;
}
}
+ /* close file */
+ close(fd);
+
+ return 0;
+}
+
+int check_pressure(t_moldyn *moldyn,t_mdrun *mdrun) {
+
+ double delta;
+
+ if(!(mdrun->sattr&SATTR_PRELAX)) {
+ return TRUE;
+ }
+
+ delta=moldyn->p_avg-moldyn->p_ref;
+
+ if(delta<0)
+ delta=-delta;
+
+ if(delta>mdrun->dp)
+ return FALSE;
+
+ return TRUE;
+}
+
+int check_temperature(t_moldyn *moldyn,t_mdrun *mdrun) {
+
+ double delta;
+
+ if(!(mdrun->sattr&SATTR_TRELAX))
+ return TRUE;
+
+ delta=moldyn->t_avg-moldyn->t_ref;
+
+ if(delta<0)
+ delta=-delta;
+
+ if(delta>mdrun->dt)
+ return FALSE;
+
+ return TRUE;
+}
+
+int displace_atom(t_moldyn *moldyn,t_mdrun *mdrun) {
+
+ t_displace_atom_params *dap;
+ t_stage *stage;
+ t_atom *atom;
+
+ stage=mdrun->stage.current->data;
+ dap=stage->params;
+
+ atom=&(moldyn->atom[dap->nr]);
+ atom->r.x+=dap->dx;
+ atom->r.y+=dap->dy;
+ atom->r.z+=dap->dz;
+
+ return 0;
+}
+
+int insert_atoms(t_moldyn *moldyn,t_mdrun *mdrun) {
+
+ t_insert_atoms_params *iap;
+ t_stage *stage;
+ t_atom *atom;
+ t_3dvec r,v,dist;
+ double d,dmin,o;
+ int cnt,i;
+ double x,y,z;
+ double x0,y0,z0;
+ u8 cr_check,run;
+
+ stage=mdrun->stage.current->data;
+ iap=stage->params;
+
+ cr_check=FALSE;
+
+ v.x=0.0; v.y=0.0; v.z=0.0;
+ x=0; y=0; z=0;
+ o=0; dmin=0;
+
+ switch(mdrun->lattice) {
+ case CUBIC:
+ o=0.5*mdrun->lc;
+ break;
+ case FCC:
+ o=0.25*mdrun->lc;
+ break;
+ case DIAMOND:
+ case ZINCBLENDE:
+ o=0.125*mdrun->lc;
+ break;
+ default:
+ break;
+ }
+
+ switch(iap->type) {
+ case INS_TOTAL:
+ x=moldyn->dim.x;
+ x0=-x/2.0;
+ y=moldyn->dim.y;
+ y0=-y/2.0;
+ z=moldyn->dim.z;
+ z0=-z/2.0;
+ cr_check=TRUE;
+ break;
+ case INS_REGION:
+ x=iap->x1-iap->x0;
+ x0=iap->x0;
+ y=iap->y1-iap->y0;
+ y0=iap->y0;
+ z=iap->z1-iap->z0;
+ z0=iap->z0;
+ cr_check=TRUE;
+ break;
+ case INS_POS:
+ x0=iap->x0;
+ y0=iap->y0;
+ z0=iap->z0;
+ cr_check=FALSE;
+ break;
+ default:
+ printf("%s unknown insertion mode: %02x\n",
+ ME,iap->type);
+ return -1;
+ }
+
+ cnt=0;
+ while(cnt<iap->ins_atoms) {
+ run=1;
+ while(run) {
+ if(iap->type!=INS_POS) {
+ r.x=rand_get_double(&(moldyn->random))*x;
+ r.y=rand_get_double(&(moldyn->random))*y;
+ r.z=rand_get_double(&(moldyn->random))*z;
+ }
+ else {
+ r.x=0.0;
+ r.y=0.0;
+ r.z=0.0;
+ }
+ r.x+=x0;
+ r.y+=y0;
+ r.z+=z0;
+ // offset
+ if(iap->type!=INS_TOTAL) {
+ r.x+=o;
+ r.y+=o;
+ r.z+=o;
+ }
+ run=0;
+ if(cr_check==TRUE) {
+ dmin=1000; // 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<(iap->cr*iap->cr)) {
+ run=1;
+ break;
+ }
+ if(d<dmin)
+ dmin=d;
+ }
+ }
+ }
+ add_atom(moldyn,iap->element,pse_mass[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);
+ cnt+=1;
+ }
+
+ return 0;
+}
+
+int chaatr(t_moldyn *moldyn,t_mdrun *mdrun) {
+
+ t_stage *stage;
+ t_chaattr_params *cap;
+ t_atom *atom;
+ int i;
+
+ stage=mdrun->stage.current->data;
+ cap=stage->params;
+
+ for(i=0;i<moldyn->count;i++) {
+ atom=&(moldyn->atom[i]);
+ if(cap->type&CHAATTR_ELEMENT) {
+ if(cap->element!=atom->element)
+ continue;
+ }
+ if(cap->type&CHAATTR_REGION) {
+ if(cap->x0<atom->r.x)
+ continue;
+ if(cap->y0<atom->r.y)
+ continue;
+ if(cap->z0<atom->r.z)
+ continue;
+ if(cap->x1>atom->r.x)
+ continue;
+ if(cap->y1>atom->r.y)
+ continue;
+ if(cap->z1>atom->r.z)
+ continue;
+ }
+ atom->attr=cap->attr;
+ }
+
+ return 0;
+}
+
+int chsattr(t_moldyn *moldyn,t_mdrun *mdrun) {
+
+ t_stage *stage;
+ t_chsattr_params *csp;
+
+ stage=mdrun->stage.current->data;
+ csp=stage->params;
+
+ if(csp->type&CHSATTR_PCTRL) {
+ if(csp->ptau>0)
+ set_p_scale(moldyn,P_SCALE_BERENDSEN,csp->ptau);
+ else
+ set_p_scale(moldyn,P_SCALE_BERENDSEN,csp->ptau);
+ }
+ 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);
+ }
+ if(csp->type&CHSATTR_PRELAX) {
+ if(csp->dp<0)
+ mdrun->sattr&=(~(SATTR_PRELAX));
+ else
+ mdrun->sattr|=SATTR_PRELAX;
+ mdrun->dp=csp->dp;
+ }
+ if(csp->type&CHSATTR_TRELAX) {
+ if(csp->dt<0)
+ mdrun->sattr&=(~(SATTR_TRELAX));
+ else
+ mdrun->sattr|=SATTR_TRELAX;
+ mdrun->dt=csp->dt;
+ }
+ if(csp->type&CHSATTR_AVGRST) {
+ if(csp->avgrst)
+ mdrun->sattr|=SATTR_AVGRST;
+ else
+ mdrun->sattr&=(~(SATTR_AVGRST));
+ }
+ if(csp->type&CHSATTR_RSTEPS) {
+ mdrun->relax_steps=csp->rsteps;
+ }
+
+ return 0;
+}
+
+#define stage_print(m) if(!(stage->executed)) \
+ printf("%s",m)
+
+int mdrun_hook(void *ptr1,void *ptr2) {
+
+ t_moldyn *moldyn;
+ t_mdrun *mdrun;
+ t_stage *stage;
+ t_list *sl;
+ int steps;
+ double tau;
+ u8 change_stage;
+
+ t_insert_atoms_params *iap;
+ t_continue_params *cp;
+ t_anneal_params *ap;
+
+ moldyn=ptr1;
+ mdrun=ptr2;
+
+ sl=&(mdrun->stage);
+
+ change_stage=FALSE;
+
+ /* return immediately if there are no more stage */
+ if(sl->current==NULL)
+ return 0;
+
+ /* get stage description */
+ stage=sl->current->data;
+
+ /* default steps and tau values */
+ steps=mdrun->relax_steps;
+ tau=mdrun->timestep;
+
+ /* check whether relaxation steps are necessary */
+ if((check_pressure(moldyn,mdrun)==TRUE)&\
+ (check_temperature(moldyn,mdrun)==TRUE)) {
+
+ /* be verbose */
+ stage_print("\n###########################\n");
+ stage_print("# [mdrun] executing stage #\n");
+ stage_print("###########################\n\n");
+
+ /* stage specific stuff */
+ switch(stage->type) {
+ case STAGE_DISPLACE_ATOM:
+ stage_print(" -> displace atom\n\n");
+ displace_atom(moldyn,mdrun);
+ change_stage=TRUE;
+ break;
+ case STAGE_INSERT_ATOMS:
+ stage_print(" -> insert atoms\n\n");
+ iap=stage->params;
+ if(iap->cnt_steps==iap->ins_steps) {
+ change_stage=TRUE;
+ break;
+ }
+ insert_atoms(moldyn,mdrun);
+ iap->cnt_steps+=1;
+ break;
+ case STAGE_CONTINUE:
+ stage_print(" -> continue\n\n");
+ if(stage->executed==TRUE) {
+ change_stage=TRUE;
+ break;
+ }
+ cp=stage->params;
+ steps=cp->runs;
+ break;
+ case STAGE_ANNEAL:
+ stage_print(" -> anneal\n\n");
+ ap=stage->params;
+ if(ap->count==ap->runs) {
+ change_stage=TRUE;
+ break;
+ }
+ if(moldyn->t_ref+ap->dt>=0.0)
+ set_temperature(moldyn,
+ moldyn->t_ref+ap->dt);
+ ap->count+=1;
+ break;
+ case STAGE_CHAATTR:
+ stage_print(" -> chaattr\n\n");
+ chaatr(moldyn,mdrun);
+ change_stage=TRUE;
+ break;
+ case STAGE_CHSATTR:
+ stage_print(" -> chsattr\n\n");
+ chsattr(moldyn,mdrun);
+ change_stage=TRUE;
+ break;
+ default:
+ printf("%s unknwon stage type\n",ME);
+ break;
+ }
+
+ /* mark as executed */
+ stage->executed=TRUE;
+
+ /* change state */
+ if(change_stage==TRUE) {
+ printf("%s finished stage\n",ME);
+ if(list_next_f(sl)==L_NO_NEXT_ELEMENT) {
+ printf("%s no more stages\n",ME);
+ return 0;
+ }
+ steps=0;
+ tau=mdrun->timestep;
+ }
+
+ }
+ else {
+
+ /* averages */
+ if(mdrun->sattr&SATTR_AVGRST)
+ average_reset(moldyn);
+
+ }
+
+ /* continue simulation */
+ moldyn_add_schedule(moldyn,steps,tau);
+
return 0;
}
t_moldyn moldyn;
t_3dvec o;
- /* clear mdrun struct */
+ /* clear structs */
memset(&mdrun,0,sizeof(t_mdrun));
+ memset(&moldyn,0,sizeof(t_moldyn));
/* parse arguments */
if(mdrun_parse_argv(&mdrun,argc,argv)<0)
return -1;
+ /* initialize list system */
+ list_init_f(&(mdrun.stage));
+
/* parse config file */
mdrun_parse_config(&mdrun);
+ /* reset the stage list */
+ list_reset_f(&(mdrun.stage));
+
/* sanity check! */
/* prepare simulation */
- moldyn_init(&moldyn,argc,argv);
+
+ if(mdrun.continue_file[0]) {
+ // read the save file
+ moldyn_read_save_file(&moldyn,mdrun.continue_file);
+ // manualaadjusting some stuff
+ moldyn.argc=argc;
+ moldyn.args=argv;
+ rand_init(&(moldyn.random),NULL,1);
+ moldyn.random.status|=RAND_STAT_VERBOSE;
+ }
+ else {
+ moldyn_init(&moldyn,argc,argv);
+ }
+
if(set_int_alg(&moldyn,mdrun.intalgo)<0)
return -1;
+
+ /* potential */
set_cutoff(&moldyn,mdrun.cutoff);
if(set_potential(&moldyn,mdrun.potential)<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,
ME,mdrun.potential);
return -1;
}
+
+ /* if it is a continue run, reset schedule and skip lattice init */
+ if(mdrun.continue_file[0]) {
+ memset(&(moldyn.schedule),0,sizeof(t_moldyn_schedule));
+ goto addsched;
+ }
+
+ /* 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);
switch(mdrun.lattice) {
case FCC:
create_lattice(&moldyn,FCC,mdrun.lc,mdrun.element1,
- mdrun.m1,0,0,mdrun.lx,
+ mdrun.m1,DEFAULT_ATOM_ATTR,0,mdrun.lx,
mdrun.ly,mdrun.lz,NULL);
break;
case DIAMOND:
create_lattice(&moldyn,DIAMOND,mdrun.lc,mdrun.element1,
- mdrun.m1,0,0,mdrun.lx,
+ mdrun.m1,DEFAULT_ATOM_ATTR,0,mdrun.lx,
mdrun.ly,mdrun.lz,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.m1,0,0,mdrun.lx,
+ mdrun.m1,DEFAULT_ATOM_ATTR,0,mdrun.lx,
mdrun.ly,mdrun.lz,&o);
o.x+=0.25*mdrun.lc; o.y=o.x; o.z=o.x;
create_lattice(&moldyn,FCC,mdrun.lc,mdrun.element2,
- mdrun.m2,0,0,mdrun.lx,
+ mdrun.m2,DEFAULT_ATOM_ATTR,1,mdrun.lx,
mdrun.ly,mdrun.lz,&o);
break;
default:
return -1;
}
moldyn_bc_check(&moldyn);
+
+ /* temperature and pressure */
set_temperature(&moldyn,mdrun.temperature);
set_pressure(&moldyn,mdrun.pressure);
thermal_init(&moldyn,TRUE);
+
+addsched:
+ /* first schedule */
moldyn_add_schedule(&moldyn,mdrun.prerun,mdrun.timestep);
+
+ /* log */
moldyn_set_log_dir(&moldyn,mdrun.sdir);
moldyn_set_report(&moldyn,"CHANGE ME","CHANGE ME TOO");
if(mdrun.elog)
set_avg_skip(&moldyn,mdrun.avgskip);
/* prepare the hook function */
+ moldyn_set_schedule_hook(&moldyn,&mdrun_hook,&mdrun);
/* run the simulation */
moldyn_integrate(&moldyn);
/* shutdown */
moldyn_shutdown(&moldyn);
+ del_stages(&mdrun);
+ list_destroy_f(&(mdrun.stage));
return 0;
}