X-Git-Url: https://hackdaworld.org/gitweb/?a=blobdiff_plain;f=mdrun.h;h=d065d5767faa6e9517a25146e7ba1d77bdd1a214;hb=97dc63eb6a519b8e1f4fbfaa9760dd94539436b0;hp=be8e2a40df51db55552df1366182de9d6eae38b1;hpb=d7f67c88195ab155f2737e57cc5e81973d3feb0c;p=physik%2Fposic.git

diff --git a/mdrun.h b/mdrun.h
index be8e2a4..d065d57 100644
--- a/mdrun.h
+++ b/mdrun.h
@@ -11,6 +11,7 @@
 #include <sys/types.h>
 #include <sys/stat.h>
 #include <fcntl.h>
+#include <unistd.h>
 
 #include <math.h>
 
@@ -40,6 +41,7 @@ typedef struct s_stage {
 	u8 executed;
 } t_stage;
 
+#define STAGE_DISPLACE_ATOM			0x00
 #define STAGE_INSERT_ATOMS			0x01
 #define STAGE_CONTINUE				0x02
 #define STAGE_ANNEAL				0x03
@@ -49,12 +51,15 @@ typedef struct s_stage {
 typedef struct s_mdrun {
 	char cfile[128];			// config file
 
+	char continue_file[128];		// moldyn save file to continue
+
 	u8 intalgo;				// integration algorithm
 	double timestep;			// timestep
 
 	u8 potential;				// potential
-
 	double cutoff;				// cutoff radius
+	double nnd;				// next neighbour distance
+
 	t_3dvec dim;				// simulation volume
 	u8 pbcx;				// periodic boundary conditions
 	u8 pbcy;
@@ -73,10 +78,8 @@ typedef struct s_mdrun {
 	u8 sattr;				// system attributes
 	double temperature;			// temperature
 	double pressure;			// pressure
-	double p_tau;				// pressure tau
-	double t_tau;				// temperature tau
-	double dp;				// delta p fpr pctrl
-	double dt;				// delta t for tctrl
+	double dp;
+	double dt;
 	int relax_steps;			// amount of relaxation steps
 
 	int prerun;				// amount of loops in first run
@@ -91,7 +94,7 @@ typedef struct s_mdrun {
 	int avgskip;				// average skip
 	char sdir[128];				// save root
 
-	t_list *stage;				// stages
+	t_list stage;				// stages
 	int s_cnt;				// stage counter
 } t_mdrun;
 
@@ -99,6 +102,11 @@ typedef struct s_mdrun {
 #define SATTR_TRELAX				0x02
 #define SATTR_AVGRST				0x04
 
+typedef struct s_displace_atom_params {
+	int nr;
+	double dx,dy,dz;
+} t_displace_atom_params;
+
 typedef struct s_insert_atoms_params {
 	u8 type;
 	double x0,y0,z0,x1,y1,z1;
@@ -108,11 +116,12 @@ typedef struct s_insert_atoms_params {
 	int ins_atoms;
 	int element;
 	u8 brand;
-	u8 aattr;
+	u8 attr;
 } t_insert_atoms_params;
 
 #define INS_TOTAL				0x01
 #define INS_REGION				0x02
+#define INS_POS					0x03
 
 typedef struct s_continue_params {
 	int runs;
@@ -138,9 +147,12 @@ typedef struct s_chaattr_params {
 
 typedef struct s_chsattr_params {
 	u8 type;
-	double tau;
-	u8 ctrl;
-	double delta;
+	double ttau;
+	double ptau;
+	double dt;
+	double dp;
+	int rsteps;
+	u8 avgrst;
 } t_chsattr_params;
 
 #define CHSATTR_PCTRL				0x01
@@ -148,6 +160,7 @@ typedef struct s_chsattr_params {
 #define CHSATTR_PRELAX				0x04
 #define CHSATTR_TRELAX				0x08
 #define CHSATTR_AVGRST				0x10
+#define CHSATTR_RSTEPS				0x20
 
 /*
  * function prototypes