X-Git-Url: https://www.hackdaworld.org/gitweb/?a=blobdiff_plain;f=moldyn.h;h=51ad482180fa44ff290109c0118dcb09b0185c09;hb=refs%2Fheads%2Forigin;hp=5b12048f908f55b3a987475dc8b352f8714ed844;hpb=0b96eb313c9bfec6272b1f8de0d99c4ce26d1686;p=physik%2Fposic.git

diff --git a/moldyn.h b/moldyn.h
index 5b12048..51ad482 100644
--- a/moldyn.h
+++ b/moldyn.h
@@ -77,6 +77,7 @@ typedef struct s_moldyn_schedule {
 /* moldyn main structure */
 typedef struct s_moldyn {
 	int count;		/* total amount of atoms */
+	double mass;		/* total system mass */
 	t_atom *atom;		/* pointer to the atoms */
 
 	t_3dvec dim;		/* dimensions of the simulation volume */
@@ -101,20 +102,31 @@ typedef struct s_moldyn {
 
 	t_linkcell lc;		/* linked cell list interface */
 
+	int avg_skip;		/* amount of steps without average calc */
+
 	double t_ref;		/* reference temperature */
 	double t;		/* actual temperature */
 	double t_sum;		/* sum over all t */
-	double mean_t;		/* mean value of t */
+	double t_avg;		/* average value of t */
+
+	t_virial gvir;		/* global virial (absolute coordinates) */
+	double gv;
+	double gv_sum;
+	double gv_avg;
 
-	t_virial virial;	/* global virial (absolute coordinates) */
 	double gp;		/* pressure computed from global virial */
 	double gp_sum;		/* sum over all gp */
-	double mean_gp;		/* mean value of gp */
+	double gp_avg;		/* average value of gp */
+
+	double virial;		/* actual virial */
+	double virial_sum;	/* sum over all calculated virials */
+	double virial_avg;	/* average of virial */
 
 	double p_ref;		/* reference pressure */
 	double p;		/* actual pressure (computed by virial) */
 	double p_sum;		/* sum over all p */
-	double mean_p;		/* mean value of p */
+	double p_avg;		/* average value of p */
+
 	t_3dvec tp;		/* thermodynamic pressure dU/dV */
 	double dv;		/* dV for thermodynamic pressure calc */
 
@@ -136,9 +148,26 @@ typedef struct s_moldyn {
 	double tau_square;	/* delta t squared */
 	int total_steps;	/* total steps */
 
+	/* energy */
 	double energy;		/* potential energy */
 	double ekin;		/* kinetic energy */
 
+	/* energy averages & fluctuations */
+	double k_sum;		/* sum of kinetic energy */
+	double v_sum;		/* sum of potential energy */
+	double k_avg;		/* average of kinetic energy */
+	double v_avg;		/* average of potential energy */
+	double k2_sum;		/* sum of kinetic energy squared */
+	double v2_sum;		/* sum of potential energy squared */
+	double k2_avg;		/* average of kinetic energy squared */
+	double v2_avg;		/* average of potential energy squared */
+	double dk2_avg;		/* mean square kinetic energy fluctuations */
+	double dv2_avg;		/* mean square potential energy fluctuations */
+	
+	/* response functions */
+	double c_v_nve;		/* constant volume heat capacity (nve) */
+	double c_v_nvt;		/* constant volume heat capacity (nvt) */
+
 	char vlsdir[128];	/* visualization/log/save directory */
 	t_visual vis;		/* visualization interface structure */
 	u8 vlsprop;		/* log/vis/save properties */
@@ -206,7 +235,9 @@ typedef struct s_moldyn {
 #define PASCAL	(NEWTON/(METER*METER))			/* N / A^2 */
 #define BAR	((1.0e5*PASCAL))			/* N / A^2 */
 #define K_BOLTZMANN	(1.380650524e-23*METER*NEWTON)	/* NA/K */
+#define K_B2		(K_BOLTZMANN*K_BOLTZMANN)	/* (NA)^2/K^2 */
 #define EV		(1.6021765314e-19*METER*NEWTON)	/* NA */
+#define JOULE		(NEWTON*METER)			/* NA */
 
 #define MOLDYN_TEMP			273.0
 #define MOLDYN_TAU			1.0
@@ -234,6 +265,10 @@ typedef struct s_moldyn {
 #define VERBOSE				1
 #define QUIET				0
 
+#define SCALE_UP			'u'
+#define SCALE_DOWN			'd'
+#define SCALE_DIRECT			'D'
+
 /*
  * potential related phsical values / constants
  *
@@ -242,35 +277,38 @@ typedef struct s_moldyn {
 #define ONE_THIRD		(1.0/3.0)
 
 #define C			0x06
+#define LC_C			3.567				/* A */
 #define M_C			12.011				/* amu */
 
 #define SI			0x0e
-#define LC_SI			(0.543105e-9*METER)		/* A */
+#define LC_SI			5.43105				/* A */
 #define M_SI			28.08553			/* amu */
 
+#define LC_3C_SIC		4.3596				/* A */
+
 #define LJ_SIGMA_SI		((0.25*sqrt(3.0)*LC_SI)/1.122462)	/* A */
 //#define LJ_SIGMA_SI		(LC_SI/1.122462)			/* A */
-//#define LJ_SIGMA_SI		(0.5*sqrt(2.0)*LC_SI/1.122462)			/* A */
+//#define LJ_SIGMA_SI		(0.5*sqrt(2.0)*LC_SI/1.122462)		/* A */
 #define LJ_EPSILON_SI		(2.1678*EV)				/* NA */
 
-#define TM_R_SI			(2.7e-10*METER)			/* A */
-#define TM_S_SI			(3.0e-10*METER)			/* A */
+#define TM_R_SI			2.7				/* A */
+#define TM_S_SI			3.0				/* A */
 #define TM_A_SI			(1830.8*EV)			/* NA */
 #define TM_B_SI			(471.18*EV)			/* NA */
-#define TM_LAMBDA_SI		(2.4799e10/METER)		/* 1/A */
-#define TM_MU_SI		(1.7322e10/METER)		/* 1/A */
+#define TM_LAMBDA_SI		2.4799				/* 1/A */
+#define TM_MU_SI		1.7322				/* 1/A */
 #define TM_BETA_SI		1.1000e-6
 #define TM_N_SI			0.78734
 #define TM_C_SI			1.0039e5
 #define TM_D_SI			16.217
 #define TM_H_SI			-0.59825
 
-#define TM_R_C			(1.8e-10*METER)			/* A */
-#define TM_S_C			(2.1e-10*METER)			/* A */
+#define TM_R_C			1.8				/* A */
+#define TM_S_C			2.1				/* A */
 #define TM_A_C			(1393.6*EV)			/* NA */
 #define TM_B_C			(346.7*EV)			/* NA */
-#define TM_LAMBDA_C		(3.4879e10/METER)		/* 1/A */
-#define TM_MU_C			(2.2119e10/METER)		/* 1/A */
+#define TM_LAMBDA_C		3.4879				/* 1/A */
+#define TM_MU_C			2.2119				/* 1/A */
 #define TM_BETA_C		1.5724e-7
 #define TM_N_C			0.72751
 #define TM_C_C			3.8049e4
@@ -279,8 +317,53 @@ typedef struct s_moldyn {
 
 #define TM_CHI_SIC		0.9776
 
+#define TM_LC_SIC		4.32				/* A */
+
+#define ALBE_R_SI		(2.82-0.14)
+#define ALBE_S_SI		(2.82+0.14)
+#define ALBE_A_SI		(3.24*EV/0.842)
+#define ALBE_B_SI		(1.842*3.24*EV/0.842)
+#define ALBE_R0_SI		2.232
+#define ALBE_LAMBDA_SI		(1.4761*sqrt(2.0*1.842))
+#define ALBE_MU_SI		(1.4761*sqrt(2.0/1.842))
+#define ALBE_GAMMA_SI		0.114354
+#define ALBE_C_SI		2.00494
+#define ALBE_D_SI		0.81472
+#define ALBE_H_SI		0.259
+
+#define ALBE_LC_SI		5.429
+
+#define ALBE_R_C		(2.00-0.15)
+#define ALBE_S_C		(2.00+0.15)
+#define ALBE_A_C		(6.00*EV/1.167)
+#define ALBE_B_C		(2.167*6.00*EV/1.167)
+#define ALBE_R0_C		1.4276
+#define ALBE_LAMBDA_C		(2.0099*sqrt(2.0*2.167))
+#define ALBE_MU_C		(2.0099*sqrt(2.0/2.167))
+#define ALBE_GAMMA_C		0.11233
+#define ALBE_C_C		181.910
+#define ALBE_D_C		6.28433
+#define ALBE_H_C		0.5556
+
+#define ALBE_LC_C		3.566
+
+#define ALBE_R_SIC		(2.40-0.20)
+#define ALBE_S_SIC		(2.40+0.10)
+#define ALBE_A_SIC		(4.36*EV/0.847)
+#define ALBE_B_SIC		(1.847*4.36*EV/0.847)
+#define ALBE_R0_SIC		1.79
+#define ALBE_LAMBDA_SIC		(1.6991*sqrt(2.0*1.847))
+#define ALBE_MU_SIC		(1.6991*sqrt(2.0/1.847))
+#define ALBE_GAMMA_SIC		0.011877
+#define ALBE_C_SIC		273987
+#define ALBE_D_SIC		180.314
+#define ALBE_H_SIC		0.68
+
+#define ALBE_LC_SIC		4.359
+
+
 /*
- * lattice constants
+ * lattice types
  */
 
 #define CUBIC			0x01
@@ -318,13 +401,15 @@ int set_potential3b_k1(t_moldyn *moldyn,pf_func3b func);
 int set_potential3b_k2(t_moldyn *moldyn,pf_func3b func);
 int set_potential_params(t_moldyn *moldyn,void *params);
 
+int set_avg_skip(t_moldyn *moldyn,int skip);
+
 int moldyn_set_log_dir(t_moldyn *moldyn,char *dir);
 int moldyn_set_report(t_moldyn *moldyn,char *author,char *title);
 int moldyn_set_log(t_moldyn *moldyn,u8 type,int timer);
 int moldyn_log_shutdown(t_moldyn *moldyn);
 
 int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass,
-                   u8 attr,u8 brand,int a,int b,int c);
+                   u8 attr,u8 brand,int a,int b,int c,t_3dvec *origin);
 int cubic_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin);
 int fcc_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin);
 int diamond_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin);
@@ -333,15 +418,19 @@ int add_atom(t_moldyn *moldyn,int element,double mass,u8 brand,u8 attr,
 int destroy_atoms(t_moldyn *moldyn);
 
 int thermal_init(t_moldyn *moldyn,u8 equi_init);
+double total_mass_calc(t_moldyn *moldyn);
 double temperature_calc(t_moldyn *moldyn);
 double get_temperature(t_moldyn *moldyn);
 int scale_velocity(t_moldyn *moldyn,u8 equi_init);
+double virial_sum(t_moldyn *moldyn);
 double pressure_calc(t_moldyn *moldyn);
+int energy_fluctuation_calc(t_moldyn *moldyn);
+int get_heat_capacity(t_moldyn *moldyn);
 double thermodynamic_pressure_calc(t_moldyn *moldyn);
 double get_pressure(t_moldyn *moldyn);
 int scale_volume(t_moldyn *moldyn);
-int scale_dim(t_moldyn *moldyn,double scale,u8 x,u8 y,u8 z);
-int scale_atoms(t_moldyn *moldyn,double scale,u8 x,u8 y,u8 z);
+int scale_dim(t_moldyn *moldyn,u8 dir,double scale,u8 x,u8 y,u8 z);
+int scale_atoms(t_moldyn *moldyn,u8 dir,double scale,u8 x,u8 y,u8 z);
 
 double e_kin_calc(t_moldyn *moldyn);
 double get_total_energy(t_moldyn *moldyn);
@@ -372,4 +461,6 @@ int check_per_bound(t_moldyn *moldyn,t_3dvec *a);
 
 int moldyn_bc_check(t_moldyn *moldyn);
 
+int get_line(int fd,char *line,int max);
+
 #endif