some initial foo checkin of posic (posic reimplemantation)

diff --git a/Makefile b/Makefile
index 8f0d97c..abffa6d 100644 (file)
--- a/Makefile
+++ b/Makefile
@@ -16,7 +16,9 @@ DEPS = moldyn.o visual/visual.o random/random.o list/list.o
 DEPS += potentials/lennard_jones.o potentials/harmonic_oscillator.o
 DEPS += potentials/tersoff.o potentials/albe.o
 
-all: sic fluctuation_calc postproc
+all: posic sic fluctuation_calc postproc
+
+posic: $(DEPS)
 
 sic: $(DEPS)
 

diff --git a/posic.c b/posic.c
index cd1a2e2..eb2db91 100644 (file)
--- a/posic.c
+++ b/posic.c
@@ -5,165 +5,37 @@
  *
  */
 
-#include <math.h>
- 
-#include "moldyn.h"
-#include "math/math.h"
-#include "init/init.h"
-#include "visual/visual.h"
+/* main include file */
 
 #include "posic.h"
 
+/* functions */
+
+
+
+/* main code */
+
+int parse_config_file() {
+
+       return 0;
+}
+
 int main(int argc,char **argv) {
 
        t_moldyn md;
 
-       t_lj_params lj;
-       t_ho_params ho;
-       t_tersoff_mult_params tp;
-
-       int a,b,c;
-       double e;
-       double help;
-       t_3dvec p;
-
-       /*
-        *  moldyn init
-        *
-        * - parsing argv
-        * - log init
-        * - random init
-        *
-        */
-       a=moldyn_init(&md,argc,argv);
-       if(a<0) return a;
-
-       /*
-        * the following overrides possibly set interaction methods by argv !!
-        */
-
-       /* params */
-       lj.sigma6=LJ_SIGMA_SI*LJ_SIGMA_SI;
-       help=lj.sigma6*lj.sigma6;
-       lj.sigma6*=help;
-       lj.sigma12=lj.sigma6*lj.sigma6;
-       lj.epsilon4=4.0*LJ_EPSILON_SI;
-       ho.equilibrium_distance=0.25*sqrt(3.0)*LC_SI;
-       ho.spring_constant=1;
-       /* assignement */
-       md.potential_force_function=lennard_jones;
-       //md.potential_force_function=harmonic_oscillator;
-       md.pot_params=&lj;
-       //md.pot_params=&ho;
-       /* cutoff radius */
-       md.cutoff=R_CUTOFF*LC_SI;
-
-       /*
-        * testing random numbers
-        */
-
-#ifdef DEBUG_RANDOM_NUMBER
-       for(a=0;a<1000000;a++)
-               printf("%f %f\n",rand_get_gauss(&(md.random)),
-                                rand_get_gauss(&(md.random)));
-       return 0;
-#endif
-
-       /*
-        * geometry & particles
-        */
-
-       /* simulation cell volume in lattice constants */
-       a=LEN_X;
-       b=LEN_Y;
-       c=LEN_Z;
-       md.dim.x=a*LC_SI;
-       md.dim.y=b*LC_SI;
-       md.dim.z=c*LC_SI;
-
-       /* (un)set to (not) get visualized 'bounding atoms' */
-       md.vis.dim.x=a*LC_SI;
-       md.vis.dim.y=b*LC_SI;
-       md.vis.dim.z=c*LC_SI;
-
-       /*
-        * particles
-        */
-
-       /* lattice init */
-
-#ifndef SIMPLE_TESTING
-       md.count=create_lattice(DIAMOND,SI,M_SI,LC_SI,a,b,c,&(md.atom));
-       printf("created silicon lattice (#atoms = %d)\n",md.count);
-#else
-       md.count=2;
-       md.atom=malloc(md.count*sizeof(t_atom));
-       md.atom[0].r.x=0.23*sqrt(3.0)*LC_SI/2.0;
-       md.atom[0].r.y=0;
-       md.atom[0].r.z=0;
-       md.atom[0].element=SI;
-       md.atom[0].mass=M_SI;
-       md.atom[1].r.x=-md.atom[0].r.x;
-       md.atom[1].r.y=0;
-       md.atom[1].r.z=0;
-       md.atom[1].element=SI;
-       md.atom[1].mass=M_SI;
-
-       //md.atom[2].r.x=0.5*(a-1)*LC_SI;
-       //md.atom[2].r.y=0.5*(b-1)*LC_SI;
-       //md.atom[2].r.z=0;
-       //md.atom[2].element=C;
-       //md.atom[2].mass=M_C;
-
-       //md.atom[3].r.x=0.5*(a-1)*LC_SI;
-       //md.atom[3].r.y=0;
-       //md.atom[3].r.z=0;
-       //md.atom[3].element=SI;
-       //md.atom[3].mass=M_SI;
-#endif
-
-       /* initial thermal fluctuations of particles */
-
-#ifndef SIMPLE_TESTING
-       printf("setting thermal fluctuations (T=%f K)\n",md.t);
-       thermal_init(&md);
-#else
-       for(a=0;a<md.count;a++) v3_zero(&(md.atom[0].v));
-       md.atom[2].v.x=-320;
-       md.atom[2].v.y=-320;
-#endif
-
-       /* check kinetic energy */
-       e=get_e_kin(md.atom,md.count);
-       printf("kinetic energy: %.40f [J]\n",e);
-       printf("3/2 N k T = %.40f [J] (T=%f [K])\n",
-              1.5*md.count*K_BOLTZMANN*md.t,md.t);
-
-       /* check total momentum */
-       p=get_total_p(md.atom,md.count);
-       printf("total momentum: %.30f [Ns]\n",v3_norm(&p));
-
-       /* check time step */
-       printf("estimated accurate time step: %.30f [s]\n",
-              estimate_time_step(&md,3.0,md.t));
-
-       /*
-        * let's do the actual md algorithm now
-        *
-        * integration of newtons equations
-        */
-
-       moldyn_integrate(&md);
-
-       printf("total energy (after integration): %.40f [J]\n",
-              get_total_energy(&md));
-
-       /* close */
-
-       link_cell_shutdown(&md);
-
-       moldyn_shutdown(&md);
-       
+       t_lj_params *lj;
+       t_ho_params *ho;
+       t_tersoff_mult_params *tp;
+       t_albe_mult_params *ap;
+
+       lj=NULL;
+       ho=NULL;
+       tp=NULL;
+       ap=NULL;
+
+
+
        return 0;
 }
 

diff --git a/posic.h b/posic.h
index 0ca2ac8..214f07d 100644 (file)
--- a/posic.h
+++ b/posic.h
@@ -1,11 +1,17 @@
 /*
  * posic.h - precipitation process of silicon carbide in silicon
  *
- * author: Frank Zirkelbach <hackbard@hackdaworl.org>
+ * author: Frank Zirkelbach <frank.zirkelbach@physik.uni-augsburg.de>
  *
  */
 
+#ifndef POSIC_H
+#define POSIC_H
+
+/* includes */
+
 #define _GNU_SOURCE
+
 #include <stdio.h>
 #include <stdlib.h>
 #include <string.h>
@@ -14,20 +20,19 @@
 #include <sys/stat.h>
 #include <fcntl.h>
 
-#ifndef POSIC_H
-#define POSIC_H
-
-#define RUNS 10000000
-//#define TAU 0.000000000000001
-#define TAU 0.000000000001
-#define WRITE_FILE 100000
+#include <math.h>
 
-#define TEMPERATURE 273.0 
+#include "math/math.h"
+#include "list/list.h"
+#include "visual/visual.h"
+#include "random/random.h"
 
-#define LEN_X 10
-#define LEN_Y 10
-#define LEN_Z 10
+#include "potentials/harmonic_oscillator.h"
+#include "potentials/lennard_jones.h"
+#include "potentials/albe.h"
+#include "potentials/tersoff_orig.h"   // obsolete & wrong! ;)
+#include "potentials/tersoff.h"
 
-#define R_CUTOFF (0.25*LEN_Z)
+/* defines */
 
 #endif