return 0;
}
-del_stages(t_mdrun *mdrun) {
+int del_stages(t_mdrun *mdrun) {
t_list *sl;
t_stage *stage;
- sl=mdrun->stage;
+ sl=&(mdrun->stage);
list_reset_f(sl);
return 0;
}
-add_stage(t_mdrun *mdrun,u8 type,void *params) {
+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;
psize=sizeof(t_chsattr_params);
break;
default:
-
+ printf("%s unknown stage type: %02x\n",ME,type);
+ return -1;
}
stage=malloc(sizeof(t_stage));
memcpy(stage->params,params,psize);
- list_add_immediate_f(mdrun->stage,stage);
+ list_add_immediate_f(&(mdrun->stage),stage);
return 0;
}
char error[128];
char line[128];
char *wptr;
- char word[16][32];
+ char word[16][64];
int wcnt;
- int i;
+ int i,o;
+ t_displace_atom_params dap;
t_insert_atoms_params iap;
t_continue_params cp;
t_anneal_params ap;
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[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],"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],"aattr",5)) {
// for aatrib line we need a special stage
// containing one schedule of 0 loops ...
- if(!strncmp(word[1],"all",3)) {
- cap.type=
-
-
- HIER WEITER
+ 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;
}
- for(i=0;i<strlen(wptr)) {
- switch(word[2][i]) {
+ 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;
}
add_stage(mdrun,STAGE_CHAATTR,&cap);
}
- else if(!strncmp(word[0],"ectrl",5)) {
- 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,word[0]);
+ printf("%s unknown keyword '%s', skipped!\n",
+ ME,word[0]);
continue;
}
}
double delta;
- if(!(mdrun->sattr&SATTR_PRELAX))
+ if(!(mdrun->sattr&SATTR_PRELAX)) {
return TRUE;
+ }
delta=moldyn->p_avg-moldyn->p_ref;
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) {
- insert_atoms_params *iap;
+ t_insert_atoms_params *iap;
t_stage *stage;
t_atom *atom;
t_3dvec r,v,dist;
- double d,dmin;
+ double d,dmin,o;
int cnt,i;
double x,y,z;
double x0,y0,z0;
u8 cr_check,run;
- stage=mdrun->stage->current->data;
+ 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=0.0;
+ x0=-x/2.0;
y=moldyn->dim.y;
- y0=0.0;
+ y0=-y/2.0;
z=moldyn->dim.z;
- z0=0.0;
+ z0=-z/2.0;
cr_check=TRUE;
break;
case INS_REGION:
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\n");
+ printf("%s unknown insertion mode: %02x\n",
+ ME,iap->type);
return -1;
}
while(cnt<iap->ins_atoms) {
run=1;
while(run) {
- r.x=(rand_get_double(&(moldyn->random))-0.5)*x+x0;
- r.y=(rand_get_double(&(moldyn->random))-0.5)*y+y0;
- r.z=(rand_get_double(&(moldyn->random))-0.5)*z+z0;
+ 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!
}
add_atom(moldyn,iap->element,pse_mass[iap->element],
iap->brand,iap->attr,&r,&v);
- printf("%s atom inserted: %f %f %f | d squared = %f\n",
- ME,r.x,r.y,r.z,dmin);
+ 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 chaatrib(t_moldyn *moldyn,t_mdrun *mdrun) {
+int chaatr(t_moldyn *moldyn,t_mdrun *mdrun) {
t_stage *stage;
t_chaattr_params *cap;
t_atom *atom;
- u8 assigne;
+ int i;
- stage=mdrun->stage->current->data;
+ stage=mdrun->stage.current->data;
cap=stage->params;
for(i=0;i<moldyn->count;i++) {
t_stage *stage;
t_chsattr_params *csp;
- stage=mdrun->stage->current->data;
+ stage=mdrun->stage.current->data;
csp=stage->params;
- switch(csp->type) {
- case CHSATTR_PCTRL:
- set_p_scale(moldyn,csp->ctrl_type,csp->tau);
- break;
- case CHSATTR_TCTRL:
- set_t_scale(moldyn,csp->ctrl_type,csp->tau);
- break;
- case CHSATTR_PRELAX:
- mdrun->sattr&=(^(SATTR_PRELAX));
- if(csp->ctrl==TRUE)
- mdrun->sattr|=SATTR_PRELAX;
- break;
- case CHSATTR_TRELAX:
- mdrun->sattr&=(^(SATTR_TRELAX));
- if(csp->ctrl==TRUE)
- mdrun->sattr|=SATTR_TRELAX;
- break;
- case CHSATTR_AVGRST:
- mdrun->sattr&=(^(SATTR_AVGRST));
- if(csp->ctrl==TRUE)
- mdrun->sattr|=SATTR_AVGRST;
- break;
- default:
- printf("%s unknown system attribute change\n",ME);
- return -1;
+ 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;
}
-int mdrun_hook(t_moldyn *moldyn,void *ptr) {
+#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;
t_continue_params *cp;
t_anneal_params *ap;
- mdrun=ptr;
- sl=mdrun->stage;
+ moldyn=ptr1;
+ mdrun=ptr2;
+
+ sl=&(mdrun->stage);
change_stage=FALSE;
return 0;
/* get stage description */
- stage=mdrun->sl->current->data;
+ 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==FALSE)|(check_temperature==FALSE))) {
+ 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;
}
insert_atoms(moldyn,mdrun);
iap->cnt_steps+=1;
- break;
+ break;
case STAGE_CONTINUE:
+ stage_print(" -> continue\n\n");
if(stage->executed==TRUE) {
change_stage=TRUE;
break;
}
cp=stage->params;
steps=cp->runs;
- break;
+ break;
case STAGE_ANNEAL:
+ stage_print(" -> anneal\n\n");
ap=stage->params;
if(ap->count==ap->runs) {
change_stage=TRUE;
break;
}
- set_temperature(moldyn,moldyn->t_ref+ap->dt);
+ if(moldyn->t_ref+ap->dt>=0.0)
+ set_temperature(moldyn,
+ moldyn->t_ref+ap->dt);
ap->count+=1;
break;
case STAGE_CHAATTR:
- chaatrib(moldyn,mdrun);
+ stage_print(" -> chaattr\n\n");
+ chaatr(moldyn,mdrun);
change_stage=TRUE;
break;
case STAGE_CHSATTR:
- chsatrib(moldyn,mdrun);
+ stage_print(" -> chsattr\n\n");
+ chsattr(moldyn,mdrun);
change_stage=TRUE;
break;
default:
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)
/* 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;
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)
moldyn_set_log(&moldyn,CREATE_REPORT,0);
set_avg_skip(&moldyn,mdrun.avgskip);
- /* pt scaling */
- if(mdrun.p_tau!=0)
- set_p_scale(&moldyn,P_SCALE_BERENDSEN,mdrun.p_tau);
- if(mdrun.t_tau!=0)
- set_t_scale(&moldyn,T_SCALE_BERENDSEN,mdrun.t_tau);
-
/* prepare the hook function */
moldyn_set_schedule_hook(&moldyn,&mdrun_hook,&mdrun);