From 4df6ed05246cf8bc9fe0cb0c8766ebc368d2f512 Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@gmail.com>
Date: Sat, 09 Mar 2019 19:33:51 +0000
Subject: [PATCH] Added stretching energy plugin
---
src/main.c | 7 +
src/plugins/Makefile.am | 6 +
src/plugins/Makefile | 18 +++++
src/plugins/Makefile.in | 18 +++++
src/plugins/stretching_energy.c | 75 +++++++++++++++++++++++++
5 files changed, 117 insertions(+), 7 deletions(-)
diff --git a/src/main.c b/src/main.c
index bf58e53..dfe7130 100644
--- a/src/main.c
+++ b/src/main.c
@@ -32,20 +32,23 @@
ts_char *plugin3 = (ts_char *)calloc(255,sizeof(ts_char));
ts_char *plugin4 = (ts_char *)calloc(255,sizeof(ts_char));
ts_char *plugin5 = (ts_char *)calloc(255,sizeof(ts_char));
+ ts_char *plugin6 = (ts_char *)calloc(255,sizeof(ts_char));
strcpy(plugin0,"/home/samo/programiranje/trisurf-ng/src/plugins/.libs/demoplugin.so");
strcpy(plugin1,"/home/samo/programiranje/trisurf-ng/src/plugins/.libs/vmdefaulthardconstraints.so");
strcpy(plugin2,"/home/samo/programiranje/trisurf-ng/src/plugins/.libs/plane_confinement.so");
strcpy(plugin3,"/home/samo/programiranje/trisurf-ng/src/plugins/.libs/pressure.so");
strcpy(plugin4,"/home/samo/programiranje/trisurf-ng/src/plugins/.libs/constant_volume.so");
strcpy(plugin5,"/home/samo/programiranje/trisurf-ng/src/plugins/.libs/constant_area.so");
- ts_char **plugins=(ts_char **)calloc(6,sizeof(ts_char *));
+ strcpy(plugin6,"/home/samo/programiranje/trisurf-ng/src/plugins/.libs/stretching_energy.so");
+ ts_char **plugins=(ts_char **)calloc(7,sizeof(ts_char *));
plugins[0]=plugin0;
plugins[1]=plugin1;
plugins[2]=plugin2;
plugins[3]=plugin3;
plugins[4]=plugin4;
plugins[5]=plugin5;
- ts_plugin_list *plist=init_plugin_list(plugins,6);
+ plugins[6]=plugin6;
+ ts_plugin_list *plist=init_plugin_list(plugins,7);
//printf("%s", plist->chain->at_start->next->plugin->filename);
//ts_fprintf(stdout, "TRISURF in PRVI PLUGIN %s\n", plist->plugin[0]->details->name);
ts_vesicle *vesicle;
diff --git a/src/plugins/Makefile b/src/plugins/Makefile
index 9b25029..28ebbd4 100644
--- a/src/plugins/Makefile
+++ b/src/plugins/Makefile
@@ -170,6 +170,13 @@
pressure_la_LINK = $(LIBTOOL) $(AM_V_lt) --tag=CC $(AM_LIBTOOLFLAGS) \
$(LIBTOOLFLAGS) --mode=link $(CCLD) $(AM_CFLAGS) $(CFLAGS) \
$(pressure_la_LDFLAGS) $(LDFLAGS) -o $@
+stretching_energy_la_LIBADD =
+am_stretching_energy_la_OBJECTS = constant_area.lo
+stretching_energy_la_OBJECTS = $(am_stretching_energy_la_OBJECTS)
+stretching_energy_la_LINK = $(LIBTOOL) $(AM_V_lt) --tag=CC \
+ $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) --mode=link $(CCLD) \
+ $(AM_CFLAGS) $(CFLAGS) $(stretching_energy_la_LDFLAGS) \
+ $(LDFLAGS) -o $@
vmdefaulthardconstraints_la_LIBADD =
am_vmdefaulthardconstraints_la_OBJECTS = default_hard_constraints.lo
vmdefaulthardconstraints_la_OBJECTS = \
@@ -215,11 +222,13 @@
SOURCES = $(constant_area_la_SOURCES) $(constant_volume_la_SOURCES) \
$(demoplugin_la_SOURCES) $(nucleus_la_SOURCES) \
$(plane_confinement_la_SOURCES) $(pressure_la_SOURCES) \
+ $(stretching_energy_la_SOURCES) \
$(vmdefaulthardconstraints_la_SOURCES)
DIST_SOURCES = $(constant_area_la_SOURCES) \
$(constant_volume_la_SOURCES) $(demoplugin_la_SOURCES) \
$(nucleus_la_SOURCES) $(plane_confinement_la_SOURCES) \
- $(pressure_la_SOURCES) $(vmdefaulthardconstraints_la_SOURCES)
+ $(pressure_la_SOURCES) $(stretching_energy_la_SOURCES) \
+ $(vmdefaulthardconstraints_la_SOURCES)
am__can_run_installinfo = \
case $$AM_UPDATE_INFO_DIR in \
n|no|NO) false;; \
@@ -368,7 +377,7 @@
top_builddir = ../..
top_srcdir = ../..
AM_CFLAGS = -Wall -Werror -DTS_VERSION=\"$(GITVERSION)\" -fgnu89-inline -Wno-error=date-time -I..
-lib_LTLIBRARIES = demoplugin.la vmdefaulthardconstraints.la nucleus.la plane_confinement.la pressure.la constant_volume.la constant_area.la
+lib_LTLIBRARIES = demoplugin.la vmdefaulthardconstraints.la nucleus.la plane_confinement.la pressure.la constant_volume.la constant_area.la stretching_energy.la
demoplugin_la_SOURCES = demo_plugin.c
demoplugin_la_LDFLAGS = -module -avoid-version -export-dynamic
vmdefaulthardconstraints_la_SOURCES = default_hard_constraints.c
@@ -383,6 +392,8 @@
constant_volume_la_LDFLAGS = -module -avoid-version -export-dynamic
constant_area_la_SOURCES = constant_area.c
constant_area_la_LDFLAGS = -module -avoid-version -export-dynamic
+stretching_energy_la_SOURCES = constant_area.c
+stretching_energy_la_LDFLAGS = -module -avoid-version -export-dynamic
all: all-am
.SUFFIXES:
@@ -470,6 +481,9 @@
pressure.la: $(pressure_la_OBJECTS) $(pressure_la_DEPENDENCIES) $(EXTRA_pressure_la_DEPENDENCIES)
$(AM_V_CCLD)$(pressure_la_LINK) -rpath $(libdir) $(pressure_la_OBJECTS) $(pressure_la_LIBADD) $(LIBS)
+stretching_energy.la: $(stretching_energy_la_OBJECTS) $(stretching_energy_la_DEPENDENCIES) $(EXTRA_stretching_energy_la_DEPENDENCIES)
+ $(AM_V_CCLD)$(stretching_energy_la_LINK) -rpath $(libdir) $(stretching_energy_la_OBJECTS) $(stretching_energy_la_LIBADD) $(LIBS)
+
vmdefaulthardconstraints.la: $(vmdefaulthardconstraints_la_OBJECTS) $(vmdefaulthardconstraints_la_DEPENDENCIES) $(EXTRA_vmdefaulthardconstraints_la_DEPENDENCIES)
$(AM_V_CCLD)$(vmdefaulthardconstraints_la_LINK) -rpath $(libdir) $(vmdefaulthardconstraints_la_OBJECTS) $(vmdefaulthardconstraints_la_LIBADD) $(LIBS)
diff --git a/src/plugins/Makefile.am b/src/plugins/Makefile.am
index b3cfafe..dacef43 100644
--- a/src/plugins/Makefile.am
+++ b/src/plugins/Makefile.am
@@ -1,5 +1,5 @@
AM_CFLAGS = -Wall -Werror -DTS_VERSION=\"$(GITVERSION)\" -fgnu89-inline -Wno-error=date-time -I..
-lib_LTLIBRARIES= demoplugin.la vmdefaulthardconstraints.la nucleus.la plane_confinement.la pressure.la constant_volume.la constant_area.la
+lib_LTLIBRARIES= demoplugin.la vmdefaulthardconstraints.la nucleus.la plane_confinement.la pressure.la constant_volume.la constant_area.la stretching_energy.la
demoplugin_la_SOURCES= demo_plugin.c
demoplugin_la_LDFLAGS = -module -avoid-version -export-dynamic
@@ -21,3 +21,7 @@
constant_area_la_SOURCES = constant_area.c
constant_area_la_LDFLAGS = -module -avoid-version -export-dynamic
+stretching_energy_la_SOURCES = constant_area.c
+stretching_energy_la_LDFLAGS = -module -avoid-version -export-dynamic
+
+
diff --git a/src/plugins/Makefile.in b/src/plugins/Makefile.in
index cd076f8..d7fca36 100644
--- a/src/plugins/Makefile.in
+++ b/src/plugins/Makefile.in
@@ -170,6 +170,13 @@
pressure_la_LINK = $(LIBTOOL) $(AM_V_lt) --tag=CC $(AM_LIBTOOLFLAGS) \
$(LIBTOOLFLAGS) --mode=link $(CCLD) $(AM_CFLAGS) $(CFLAGS) \
$(pressure_la_LDFLAGS) $(LDFLAGS) -o $@
+stretching_energy_la_LIBADD =
+am_stretching_energy_la_OBJECTS = constant_area.lo
+stretching_energy_la_OBJECTS = $(am_stretching_energy_la_OBJECTS)
+stretching_energy_la_LINK = $(LIBTOOL) $(AM_V_lt) --tag=CC \
+ $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) --mode=link $(CCLD) \
+ $(AM_CFLAGS) $(CFLAGS) $(stretching_energy_la_LDFLAGS) \
+ $(LDFLAGS) -o $@
vmdefaulthardconstraints_la_LIBADD =
am_vmdefaulthardconstraints_la_OBJECTS = default_hard_constraints.lo
vmdefaulthardconstraints_la_OBJECTS = \
@@ -215,11 +222,13 @@
SOURCES = $(constant_area_la_SOURCES) $(constant_volume_la_SOURCES) \
$(demoplugin_la_SOURCES) $(nucleus_la_SOURCES) \
$(plane_confinement_la_SOURCES) $(pressure_la_SOURCES) \
+ $(stretching_energy_la_SOURCES) \
$(vmdefaulthardconstraints_la_SOURCES)
DIST_SOURCES = $(constant_area_la_SOURCES) \
$(constant_volume_la_SOURCES) $(demoplugin_la_SOURCES) \
$(nucleus_la_SOURCES) $(plane_confinement_la_SOURCES) \
- $(pressure_la_SOURCES) $(vmdefaulthardconstraints_la_SOURCES)
+ $(pressure_la_SOURCES) $(stretching_energy_la_SOURCES) \
+ $(vmdefaulthardconstraints_la_SOURCES)
am__can_run_installinfo = \
case $$AM_UPDATE_INFO_DIR in \
n|no|NO) false;; \
@@ -368,7 +377,7 @@
top_builddir = @top_builddir@
top_srcdir = @top_srcdir@
AM_CFLAGS = -Wall -Werror -DTS_VERSION=\"$(GITVERSION)\" -fgnu89-inline -Wno-error=date-time -I..
-lib_LTLIBRARIES = demoplugin.la vmdefaulthardconstraints.la nucleus.la plane_confinement.la pressure.la constant_volume.la constant_area.la
+lib_LTLIBRARIES = demoplugin.la vmdefaulthardconstraints.la nucleus.la plane_confinement.la pressure.la constant_volume.la constant_area.la stretching_energy.la
demoplugin_la_SOURCES = demo_plugin.c
demoplugin_la_LDFLAGS = -module -avoid-version -export-dynamic
vmdefaulthardconstraints_la_SOURCES = default_hard_constraints.c
@@ -383,6 +392,8 @@
constant_volume_la_LDFLAGS = -module -avoid-version -export-dynamic
constant_area_la_SOURCES = constant_area.c
constant_area_la_LDFLAGS = -module -avoid-version -export-dynamic
+stretching_energy_la_SOURCES = constant_area.c
+stretching_energy_la_LDFLAGS = -module -avoid-version -export-dynamic
all: all-am
.SUFFIXES:
@@ -470,6 +481,9 @@
pressure.la: $(pressure_la_OBJECTS) $(pressure_la_DEPENDENCIES) $(EXTRA_pressure_la_DEPENDENCIES)
$(AM_V_CCLD)$(pressure_la_LINK) -rpath $(libdir) $(pressure_la_OBJECTS) $(pressure_la_LIBADD) $(LIBS)
+stretching_energy.la: $(stretching_energy_la_OBJECTS) $(stretching_energy_la_DEPENDENCIES) $(EXTRA_stretching_energy_la_DEPENDENCIES)
+ $(AM_V_CCLD)$(stretching_energy_la_LINK) -rpath $(libdir) $(stretching_energy_la_OBJECTS) $(stretching_energy_la_LIBADD) $(LIBS)
+
vmdefaulthardconstraints.la: $(vmdefaulthardconstraints_la_OBJECTS) $(vmdefaulthardconstraints_la_DEPENDENCIES) $(EXTRA_vmdefaulthardconstraints_la_DEPENDENCIES)
$(AM_V_CCLD)$(vmdefaulthardconstraints_la_LINK) -rpath $(libdir) $(vmdefaulthardconstraints_la_OBJECTS) $(vmdefaulthardconstraints_la_LIBADD) $(LIBS)
diff --git a/src/plugins/stretching_energy.c b/src/plugins/stretching_energy.c
new file mode 100644
index 0000000..fd44c52
--- /dev/null
+++ b/src/plugins/stretching_energy.c
@@ -0,0 +1,75 @@
+#include <stdlib.h>
+#include<math.h>
+
+#include "general.h"
+#include "vertex.h"
+#include "cell.h"
+#include "vesicle.h"
+#include "frame.h"
+char plugin_name[] = "Stretching energy";
+char plugin_description[]= "Plugin adds stretching energy to Monte Carlo steps";
+char plugin_author[] = "SAMO PENIC";
+
+
+typedef struct {
+ ts_double dstretchenergy;
+ ts_double A0;
+ ts_double epsarea;
+} plugin_data;
+
+
+ts_plugin_details *init (){
+ ts_plugin_details *details=(ts_plugin_details *)calloc(1,sizeof(ts_plugin_details));
+ details->name = plugin_name;
+ details->data = (plugin_data *)calloc(1,sizeof(plugin_data)); //storing data
+ return details;
+}
+
+
+/*
+ts_vesicle *after_vesicle_init(ts_vesicle *vesicle){
+ plugin_data *data=(plugin_data *)vesicle->plist->pointer->plugin->details->data;
+ ts_fprintf(stdout,"area volume initialized\n");
+ centermass(vesicle);
+ cell_occupation(vesicle);
+ vesicle_area(vesicle);
+ data->A0=vesicle->area;
+ data->epsarea=data->A0/(ts_double)vesicle->tlist->n;
+ return vesicle;
+}
+*/
+
+void vm_energy_before_prepare(ts_vesicle *vesicle, ts_vertex *vtx){
+ if(vesicle->tape->stretchswitch==1){
+ plugin_data *data=(plugin_data *)vesicle->plist->pointer->plugin->details->data;
+ ts_uint i;
+ data->dstretchenergy=0.0;
+ for(i=0;i<vtx->tristar_no;i++) data->dstretchenergy-=vtx->tristar[i]->energy;
+ }
+}
+
+
+ts_double vm_energy_after_execute(ts_vesicle *vesicle, ts_vertex *vtx){
+ //stretching energy 2 of 3
+ if(vesicle->tape->stretchswitch==1){
+ plugin_data *data=(plugin_data *)vesicle->plist->pointer->plugin->details->data;
+ ts_uint i;
+ for(i=0;i<vtx->tristar_no;i++){
+ stretchenergy(vesicle, vtx->tristar[i]);
+ data->dstretchenergy+=vtx->tristar[i]->energy;
+ }
+ }
+ return data->dstretchenergy;
+}
+
+
+
+void vm_new_state_rejected(ts_vesicle *vesicle, ts_vertex *vtx, ts_vertex *old_vtx){
+ //stretching energy 3 of 3
+ if(vesicle->tape->stretchswitch==1){
+ ts_uint i;
+ for(i=0;i<vtx->tristar_no;i++){
+ stretchenergy(vesicle,vtx->tristar[i]);
+ }
+ }
+}
--
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