#include <math.h>
#include "moldyn.h"
-#include "math/math.h"
-#include "init/init.h"
-#include "visual/visual.h"
-
#include "posic.h"
+/* potential */
+#include "potentials/harmonic_oscillator.h"
+#include "potentials/lennard_jones.h"
+#include "potentials/albe.h"
+
+#ifdef TERSOFF_ORIG
+#include "potentials/tersoff_orig.h"
+#else
+#include "potentials/tersoff.h"
+#endif
+
+#define INJECT 1
+#define NR_ATOMS 4
+
+int hook(void *moldyn,void *hook_params) {
+
+ t_moldyn *md;
+ t_3dvec r,v,dist;
+ double d;
+ unsigned char run;
+ int i,j;
+ t_atom *atom;
+
+ md=moldyn;
+
+// vortrag
+set_temperature(moldyn,(4-md->schedule.count)*1000.0);
+set_pt_scale(md,0,0,T_SCALE_BERENDSEN,100.0);
+
+return 0;
+
+ printf("\nschedule hook: ");
+
+ if(!(md->schedule.count%2)) {
+ /* add carbon at random place, and enable t scaling */
+ for(j=0;j<NR_ATOMS;j++) {
+ run=1;
+ while(run) {
+ r.x=rand_get_double(&(md->random))*md->dim.x;
+ r.y=rand_get_double(&(md->random))*md->dim.y;
+ r.z=rand_get_double(&(md->random))*md->dim.z;
+ for(i=0;i<md->count;i++) {
+ atom=&(md->atom[i]);
+ v3_sub(&dist,&(atom->r),&r);
+ d=v3_absolute_square(&dist);
+ if(d>TM_R_C)
+ run=0;
+ }
+ }
+ v.x=0; v.y=0; v.z=0;
+ add_atom(md,C,M_C,1,
+ ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
+ &r,&v);
+ }
+ printf("adding atoms & enable t scaling\n");
+ set_pt_scale(md,0,0,T_SCALE_BERENDSEN,100.0);
+ }
+ else {
+ /* disable t scaling */
+ printf("disabling t scaling\n");
+ set_pt_scale(md,0,0,0,0);
+ }
+
+ return 0;
+}
+
int main(int argc,char **argv) {
+ /* check argv */
+ if(argc!=3) {
+ printf("[sic] usage: %s <logdir> <temperatur>\n",argv[0]);
+ return -1;
+ }
+
/* main moldyn structure */
t_moldyn md;
/* potential parameters */
- t_lj_params lj;
- t_ho_params ho;
t_tersoff_mult_params tp;
+ t_albe_mult_params ap;
- /* misc variables, mainly to initialize stuff */
- t_3dvec r,v;
+ /* atom injection counter */
+ int inject;
- /* temperature */
- double t;
+ /* testing location & velocity vector */
+ t_3dvec r,v;
+ memset(&r,0,sizeof(t_3dvec));
+ memset(&v,0,sizeof(t_3dvec));
/* initialize moldyn */
- printf("[sic] moldyn init\n");
moldyn_init(&md,argc,argv);
/* choose integration algorithm */
- printf("[sic] setting integration algorithm\n");
set_int_alg(&md,MOLDYN_INTEGRATE_VERLET);
/* choose potential */
- printf("[sic] selecting potential\n");
- //set_potential1b(&md,tersoff_mult_1bp,&tp);
- //set_potential2b(&md,tersoff_mult_2bp,&tp);
- //set_potential3b(&md,tersoff_mult_3bp,&tp);
- set_potential2b(&md,lennard_jones,&lj);
+#ifdef ALBE
+ set_potential3b_j1(&md,albe_mult_3bp_j1);
+ set_potential3b_k1(&md,albe_mult_3bp_k1);
+ set_potential3b_j2(&md,albe_mult_3bp_j2);
+ set_potential3b_k2(&md,albe_mult_3bp_k2);
+#else
+ set_potential1b(&md,tersoff_mult_1bp);
+ set_potential3b_j1(&md,tersoff_mult_3bp_j1);
+ set_potential3b_k1(&md,tersoff_mult_3bp_k1);
+ set_potential3b_j2(&md,tersoff_mult_3bp_j2);
+ set_potential3b_k2(&md,tersoff_mult_3bp_k2);
+#endif
+
+#ifdef ALBE
+ set_potential_params(&md,&ap);
+#else
+ set_potential_params(&md,&tp);
+#endif
+
+ /* cutoff radius */
+#ifdef ALBE
+ set_cutoff(&md,ALBE_S_SI);
+#else
+ set_cutoff(&md,TM_S_SI);
+#endif
/*
* potential parameters
*/
- /* lennard jones */
- lj.sigma6=LJ_SIGMA_SI*LJ_SIGMA_SI*LJ_SIGMA_SI;
- lj.sigma6*=lj.sigma6;
- lj.sigma12=lj.sigma6*lj.sigma6;
- lj.epsilon4=4.0*LJ_EPSILON_SI;
+ /*
+ * tersoff mult potential parameters for SiC
+ */
+ tp.S[0]=TM_S_SI;
+ tp.R[0]=TM_R_SI;
+ tp.A[0]=TM_A_SI;
+ tp.B[0]=TM_B_SI;
+ tp.lambda[0]=TM_LAMBDA_SI;
+ tp.mu[0]=TM_MU_SI;
+ tp.beta[0]=TM_BETA_SI;
+ tp.n[0]=TM_N_SI;
+ tp.c[0]=TM_C_SI;
+ tp.d[0]=TM_D_SI;
+ tp.h[0]=TM_H_SI;
+
+ tp.S[1]=TM_S_C;
+ tp.R[1]=TM_R_C;
+ tp.A[1]=TM_A_C;
+ tp.B[1]=TM_B_C;
+ tp.lambda[1]=TM_LAMBDA_C;
+ tp.mu[1]=TM_MU_C;
+ tp.beta[1]=TM_BETA_C;
+ tp.n[1]=TM_N_C;
+ tp.c[1]=TM_C_C;
+ tp.d[1]=TM_D_C;
+ tp.h[1]=TM_H_C;
- /* harmonic oscillator */
- ho.equilibrium_distance=0.25*sqrt(3.0)*LC_SI;
- ho.spring_constant=1;
+ tp.chi=TM_CHI_SIC;
- /* cutoff radius */
- printf("[sic] setting cutoff radius\n");
- set_cutoff(&md,5*LC_SI);
+ tersoff_mult_complete_params(&tp);
+
+ /*
+ * albe mult potential parameters for SiC
+ */
+ ap.S[0]=ALBE_S_SI;
+ ap.R[0]=ALBE_R_SI;
+ ap.A[0]=ALBE_A_SI;
+ ap.B[0]=ALBE_B_SI;
+ ap.r0[0]=ALBE_R0_SI;
+ ap.lambda[0]=ALBE_LAMBDA_SI;
+ ap.mu[0]=ALBE_MU_SI;
+ ap.gamma[0]=ALBE_GAMMA_SI;
+ ap.c[0]=ALBE_C_SI;
+ ap.d[0]=ALBE_D_SI;
+ ap.h[0]=ALBE_H_SI;
+
+ ap.S[1]=ALBE_S_C;
+ ap.R[1]=ALBE_R_C;
+ ap.A[1]=ALBE_A_C;
+ ap.B[1]=ALBE_B_C;
+ ap.r0[1]=ALBE_R0_C;
+ ap.lambda[1]=ALBE_LAMBDA_C;
+ ap.mu[1]=ALBE_MU_C;
+ ap.gamma[1]=ALBE_GAMMA_C;
+ ap.c[1]=ALBE_C_C;
+ ap.d[1]=ALBE_D_C;
+ ap.h[1]=ALBE_H_C;
+
+ ap.Smixed=ALBE_S_SIC;
+ ap.Rmixed=ALBE_R_SIC;
+ ap.Amixed=ALBE_A_SIC;
+ ap.Bmixed=ALBE_B_SIC;
+ ap.r0_mixed=ALBE_R0_SIC;
+ ap.lambda_m=ALBE_LAMBDA_SIC;
+ ap.mu_m=ALBE_MU_SIC;
+ ap.gamma_m=ALBE_GAMMA_SIC;
+ ap.c_mixed=ALBE_C_SIC;
+ ap.d_mixed=ALBE_D_SIC;
+ ap.h_mixed=ALBE_H_SIC;
+
+ albe_mult_complete_params(&ap);
/* set (initial) dimensions of simulation volume */
- printf("[sic] setting dimensions\n");
- set_dim(&md,10*LC_SI,10*LC_SI,10*LC_SI,TRUE);
+ set_dim(&md,6*LC_SI_ALBE,6*LC_SI_ALBE,6*LC_SI_ALBE,TRUE);
+ //set_dim(&md,6*LC_SI,6*LC_SI,6*LC_SI,TRUE);
+ //set_dim(&md,6*LC_C_ALBE,6*LC_C_ALBE,6*LC_C_ALBE,TRUE);
+ //set_dim(&md,6*LC_C,6*LC_C,6*LC_C,TRUE);
+ //set_dim(&md,6*LC_SIC_ALBE,6*LC_SIC_ALBE,6*LC_SIC_ALBE,TRUE);
/* set periodic boundary conditions in all directions */
- printf("[sic] setting periodic boundary conditions\n");
set_pbc(&md,TRUE,TRUE,TRUE);
/* create the lattice / place atoms */
- printf("[sic] creating atoms\n");
- //memset(&v,0,sizeof(t_3dvec));
- //r.y=0;
- //r.z=0;
- //r.x=0.23*sqrt(3.0)*LC_SI/2.0;
- //add_atom(&md,SI,M_SI,0,ATOM_ATTR_2BP,&r,&v);
- //r.x=-r.x;
- //add_atom(&md,SI,M_SI,0,ATOM_ATTR_2BP,&r,&v);
- create_lattice(&md,DIAMOND,LC_SI,SI,M_SI,ATOM_ATTR_2BP,0,10,10,10);
-
- /* set temperature */
- printf("[sic] setting temperature\n");
- set_temperature(&md,0.0);
+ //create_lattice(&md,DIAMOND,LC_SI,SI,M_SI,
+ //create_lattice(&md,DIAMOND,LC_C_ALBE,C,M_C,
+ create_lattice(&md,DIAMOND,LC_SI_ALBE,SI,M_SI,
+ ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
+ // ATOM_ATTR_2BP|ATOM_ATTR_HB,
+ 0,6,6,6,NULL);
+ // 1,6,6,6,NULL);
+
+ /* create centered zinc blende lattice */
+ /*
+ r.x=0.5*0.25*LC_SIC_ALBE; r.y=r.x; r.z=r.x;
+ create_lattice(&md,FCC,LC_SIC_ALBE,SI,M_SI,
+ ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
+ 0,6,6,6,&r);
+ r.x+=0.25*LC_SIC_ALBE; r.y=r.x; r.z=r.x;
+ create_lattice(&md,FCC,LC_SIC_ALBE,C,M_C,
+ ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
+ 1,6,6,6,&r);
+ */
+
+ moldyn_bc_check(&md);
+
+ /* testing configuration */
+ //r.x=0.27*sqrt(3.0)*LC_SI/2.0; v.x=0;
+ //r.x=(TM_S_SI+TM_R_SI)/4.0; v.x=0;
+ //r.y=0; v.y=0;
+ //r.z=0; v.z=0;
+ //add_atom(&md,SI,M_SI,0,
+ // ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
+ // ATOM_ATTR_2BP|ATOM_ATTR_HB,
+ // &r,&v);
+ //r.x=-r.x; v.x=-v.x;
+ //r.y=0; v.y=0;
+ //r.z=0; v.z=0;
+ //add_atom(&md,SI,M_SI,0,
+ // ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
+ // ATOM_ATTR_2BP|ATOM_ATTR_HB,
+ // &r,&v);
+ //r.z=0.27*sqrt(3.0)*LC_SI/2.0; v.z=0;
+ //r.x=(TM_S_SI+TM_R_SI)/4.0; v.x=0;
+ //r.y=0; v.y=0;
+ //r.x=0; v.x=0;
+ //add_atom(&md,SI,M_SI,0,
+ // ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
+ // ATOM_ATTR_2BP|ATOM_ATTR_HB,
+ // &r,&v);
+ //r.z=-r.z; v.z=-v.z;
+ //r.y=0; v.y=0;
+ //r.x=0; v.x=0;
+ //add_atom(&md,SI,M_SI,0,
+ // ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
+ // ATOM_ATTR_2BP|ATOM_ATTR_HB,
+ // &r,&v);
+
+ /* set temperature & pressure */
+ set_temperature(&md,atof(argv[2])+273.0);
+ set_pressure(&md,BAR);
+
+ /* set p/t scaling */
+ //set_pt_scale(&md,P_SCALE_BERENDSEN,0.001,
+ // T_SCALE_BERENDSEN,100.0);
+ //set_pt_scale(&md,0,0,T_SCALE_DIRECT,1.0);
+ //set_pt_scale(&md,P_SCALE_BERENDSEN,0.001,0,0);
- /* initial thermal fluctuations of particles */
- printf("[sic] thermal init\n");
- thermal_init(&md);
+ /* initial thermal fluctuations of particles (in equilibrium) */
+ thermal_init(&md,TRUE);
/* create the simulation schedule */
- printf("[sic] adding schedule\n");
- moldyn_add_schedule(&md,10000,1.0e-15);
+ /* initial configuration */
+ moldyn_add_schedule(&md,10000,1.0);
+ //moldyn_add_schedule(&md,1000,1.0);
+ //moldyn_add_schedule(&md,1000,1.0);
+ //moldyn_add_schedule(&md,1000,1.0);
+ //moldyn_add_schedule(&md,1000,1.0);
+ //moldyn_add_schedule(&md,1000,1.0);
+ /* adding atoms */
+ //for(inject=0;inject<INJECT;inject++) {
+ // /* injecting atom and run with enabled t scaling */
+ // moldyn_add_schedule(&md,900,1.0);
+ // /* continue running with disabled t scaling */
+ // moldyn_add_schedule(&md,1100,1.0);
+ //}
+
+
+ /* schedule hook function */
+ moldyn_set_schedule_hook(&md,&hook,NULL);
/* activate logging */
- printf("[sic] activate logging\n");
- moldyn_set_log(&md,LOG_TOTAL_ENERGY,"saves/test-energy",100);
- moldyn_set_log(&md,VISUAL_STEP,"saves/test-visual",100);
+ moldyn_set_log_dir(&md,argv[1]);
+ moldyn_set_report(&md,"Frank Zirkelbach","Test 1");
+ moldyn_set_log(&md,LOG_TOTAL_ENERGY,1);
+ moldyn_set_log(&md,LOG_TEMPERATURE,1);
+ moldyn_set_log(&md,LOG_PRESSURE,1);
+ moldyn_set_log(&md,VISUAL_STEP,100);
+ moldyn_set_log(&md,SAVE_STEP,100);
+ moldyn_set_log(&md,CREATE_REPORT,0);
/*
* let's do the actual md algorithm now
*
* integration of newtons equations
*/
-
- printf("[sic] integration start, go get a coffee ...\n");
moldyn_integrate(&md);
+#ifdef DEBUG
+return 0;
+#endif
- /* close */
+ /*
+ * post processing the data
+ */
- printf("[sic] shutdown\n");
+ /* response functions expressed by energy fluctuations */
+ calc_fluctuations(1000.0,9999.0,&md);
+ get_heat_capacity(&md);
+
+ /* close */
moldyn_shutdown(&md);
return 0;
projects / physik / posic.git / blobdiff