introduced albe_orig (much faster!) + small change for c2, d2, c2/d2 ...

[physik/posic.git] / mdrun.c

diff --git a/mdrun.c b/mdrun.c
index b2e67f3..907388a 100644 (file)
--- a/mdrun.c
+++ b/mdrun.c
@@ -11,6 +11,7 @@
 #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
@@ -90,6 +91,9 @@ int add_stage(t_mdrun *mdrun,u8 type,void *params) {
        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;
@@ -138,10 +142,11 @@ int mdrun_parse_config(t_mdrun *mdrun) {
        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;
@@ -185,13 +190,15 @@ int mdrun_parse_config(t_mdrun *mdrun) {
                                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))
@@ -199,6 +206,8 @@ int mdrun_parse_config(t_mdrun *mdrun) {
                        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))
@@ -368,7 +377,14 @@ int mdrun_parse_config(t_mdrun *mdrun) {
                        mdrun->visualize=atoi(word[1]);
                else if(!strncmp(word[0],"stage",5)) {
                        // for every stage line, add a stage
-                       if(!strncmp(word[1],"ins_atoms",9)) {
+                       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]);
@@ -494,6 +510,23 @@ int check_temperature(t_moldyn *moldyn,t_mdrun *mdrun) {
        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;
@@ -742,6 +775,11 @@ int mdrun_hook(void *ptr1,void *ptr2) {
                
                /* 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;
@@ -751,7 +789,7 @@ int mdrun_hook(void *ptr1,void *ptr2) {
                                }
                                insert_atoms(moldyn,mdrun);
                                iap->cnt_steps+=1;
-                                       break;
+                               break;
                        case STAGE_CONTINUE:
                                stage_print("  -> continue\n\n");
                                if(stage->executed==TRUE) {
@@ -760,7 +798,7 @@ int mdrun_hook(void *ptr1,void *ptr2) {
                                }
                                cp=stage->params;
                                steps=cp->runs;
-                                       break;
+                               break;
                        case STAGE_ANNEAL:
                                stage_print("  -> anneal\n\n");
                                ap=stage->params;
@@ -843,9 +881,24 @@ int main(int argc,char **argv) {
        /* 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;
@@ -855,6 +908,11 @@ int main(int argc,char **argv) {
                                             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,
@@ -871,6 +929,14 @@ int main(int argc,char **argv) {
                               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) {
@@ -900,10 +966,17 @@ int main(int argc,char **argv) {
                        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)