From bac0042f1ec44a174741f05b218ddde48108b3f2 Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@gmail.com>
Date: Tue, 31 May 2016 20:23:29 +0000
Subject: [PATCH] Fix in vertexmove. Macro was not working
---
src/main.c | 2 +-
src/tape | 8 ++++----
src/vertexmove.c | 10 ++++++----
3 files changed, 11 insertions(+), 9 deletions(-)
diff --git a/src/main.c b/src/main.c
index 1fe6618..72e2b74 100644
--- a/src/main.c
+++ b/src/main.c
@@ -55,7 +55,6 @@
}
fclose(fd);
start_iteration++;
- printf("nucleus coords: %.17e %.17e %.17e\n",vesicle->nucleus_center[0], vesicle->nucleus_center[1], vesicle->nucleus_center[2]);
}
else
ts_fprintf(stdout,"No .status file. The iteration count will start from 0");
@@ -123,6 +122,7 @@
}
}
}
+ //printf("nucleus coords: %.17e %.17e %.17e\n",vesicle->nucleus_center[0], vesicle->nucleus_center[1], vesicle->nucleus_center[2]);
run_simulation(vesicle, tape->mcsweeps, tape->inititer, tape->iterations, start_iteration);
write_master_xml_file(command_line_args.output_fullfilename);
diff --git a/src/tape b/src/tape
index 12f88cd..dc425e4 100644
--- a/src/tape
+++ b/src/tape
@@ -42,9 +42,9 @@
####### Nucleus (inside the vesicle) ###########
# Radius of an impenetrable hard sphere inside the vesicle
R_nucleus=0
-R_nucleusX=2.0
-R_nucleusY=6.0
-R_nucleusZ=2.0
+R_nucleusX=6.0
+R_nucleusY=12.0
+R_nucleusZ=6.0
####### Cell definitions ############
nxmax=60
nymax=60
@@ -54,7 +54,7 @@
####### Program Control ############
#how many MC sweeps between subsequent records of states to disk
#200000
-mcsweeps=20
+mcsweeps=200
#how many initial mcsweeps*inititer MC sweeps before recording to disk?
#2
inititer=0
diff --git a/src/vertexmove.c b/src/vertexmove.c
index 5a51c10..fb74a06 100644
--- a/src/vertexmove.c
+++ b/src/vertexmove.c
@@ -72,21 +72,23 @@
// TODO: Maybe faster if checks only nucleus-neighboring cells
// Nucleus penetration check:
-#define SQ(x) x*x
+//#define SQ(x) x*x
if(vesicle->R_nucleus>0.0){
- if (SQ(vtx->x-vesicle->nucleus_center[0])+ SQ(vtx->y-vesicle->nucleus_center[1]) + SQ(vtx->z-vesicle->nucleus_center[2]) < vesicle->R_nucleus){
+ if ((vtx->x-vesicle->nucleus_center[0])*(vtx->x-vesicle->nucleus_center[0])+ (vtx->y-vesicle->nucleus_center[1])*(vtx->y-vesicle->nucleus_center[1]) + (vtx->z-vesicle->nucleus_center[2])*(vtx->z-vesicle->nucleus_center[2]) < vesicle->R_nucleus){
vtx=memcpy((void *)vtx,(void *)&backupvtx[0],sizeof(ts_vertex));
return TS_FAIL;
}
} else if(vesicle->R_nucleusX>0.0){
// fprintf(stderr,"DEBUG, (Rx, Ry,Rz)^2=(%f,%f,%f)\n",vesicle->R_nucleusX, vesicle->R_nucleusY, vesicle->R_nucleusZ);
- if (SQ(vtx->x-vesicle->nucleus_center[0])/vesicle->R_nucleusX + SQ(vtx->y-vesicle->nucleus_center[1])/vesicle->R_nucleusY + SQ(vtx->z-vesicle->nucleus_center[2])/vesicle->R_nucleusZ < 1.0){
+// if (SQ(vtx->x-vesicle->nucleus_center[0])/vesicle->R_nucleusX + SQ(vtx->y-vesicle->nucleus_center[1])/vesicle->R_nucleusY + SQ(vtx->z-vesicle->nucleus_center[2])/vesicle->R_nucleusZ < 1.0){
+ if ((vtx->x-vesicle->nucleus_center[0])*(vtx->x-vesicle->nucleus_center[0])/vesicle->R_nucleusX + (vtx->y-vesicle->nucleus_center[1])*(vtx->y-vesicle->nucleus_center[1])/vesicle->R_nucleusY + (vtx->z-vesicle->nucleus_center[2])*(vtx->z-vesicle->nucleus_center[2])/vesicle->R_nucleusZ < 1.0){
+// if (SQ(vtx->x)/vesicle->R_nucleusX + SQ(vtx->y)/vesicle->R_nucleusY + SQ(vtx->z)/vesicle->R_nucleusZ < 1.0){
vtx=memcpy((void *)vtx,(void *)&backupvtx[0],sizeof(ts_vertex));
return TS_FAIL;
}
}
-#undef SQ
+//#undef SQ
//self avoidance check with distant vertices
cellidx=vertex_self_avoidance(vesicle, vtx);
//check occupation number
--
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