From 2c4278db6ead5c27e30a3000097ed898c968534e Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@gmail.com>
Date: Sat, 09 Mar 2019 19:45:22 +0000
Subject: [PATCH] Added direct force plugin and fixes in stretching energy
---
src/main.c | 7 +
src/plugins/Makefile.am | 6 +
src/plugins/Makefile | 31 +++++++--
src/plugins/Makefile.in | 31 +++++++--
src/vertexmove.c | 31 ---------
src/plugins/direct_force_on_c0.c | 22 +++++++
src/plugins/stretching_energy.c | 9 +-
7 files changed, 83 insertions(+), 54 deletions(-)
diff --git a/src/main.c b/src/main.c
index dfe7130..ecf9678 100644
--- a/src/main.c
+++ b/src/main.c
@@ -33,6 +33,7 @@
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));
+ ts_char *plugin7 = (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");
@@ -40,7 +41,8 @@
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");
strcpy(plugin6,"/home/samo/programiranje/trisurf-ng/src/plugins/.libs/stretching_energy.so");
- ts_char **plugins=(ts_char **)calloc(7,sizeof(ts_char *));
+ strcpy(plugin7,"/home/samo/programiranje/trisurf-ng/src/plugins/.libs/direct_force_on_c0.so");
+ ts_char **plugins=(ts_char **)calloc(8,sizeof(ts_char *));
plugins[0]=plugin0;
plugins[1]=plugin1;
plugins[2]=plugin2;
@@ -48,7 +50,8 @@
plugins[4]=plugin4;
plugins[5]=plugin5;
plugins[6]=plugin6;
- ts_plugin_list *plist=init_plugin_list(plugins,7);
+ plugins[7]=plugin7;
+ ts_plugin_list *plist=init_plugin_list(plugins,8);
//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 28ebbd4..c1d5e65 100644
--- a/src/plugins/Makefile
+++ b/src/plugins/Makefile
@@ -151,6 +151,13 @@
demoplugin_la_LINK = $(LIBTOOL) $(AM_V_lt) --tag=CC $(AM_LIBTOOLFLAGS) \
$(LIBTOOLFLAGS) --mode=link $(CCLD) $(AM_CFLAGS) $(CFLAGS) \
$(demoplugin_la_LDFLAGS) $(LDFLAGS) -o $@
+direct_force_on_c0_la_LIBADD =
+am_direct_force_on_c0_la_OBJECTS = direct_force_on_c0.lo
+direct_force_on_c0_la_OBJECTS = $(am_direct_force_on_c0_la_OBJECTS)
+direct_force_on_c0_la_LINK = $(LIBTOOL) $(AM_V_lt) --tag=CC \
+ $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) --mode=link $(CCLD) \
+ $(AM_CFLAGS) $(CFLAGS) $(direct_force_on_c0_la_LDFLAGS) \
+ $(LDFLAGS) -o $@
nucleus_la_LIBADD =
am_nucleus_la_OBJECTS = nucleus.lo
nucleus_la_OBJECTS = $(am_nucleus_la_OBJECTS)
@@ -171,7 +178,7 @@
$(LIBTOOLFLAGS) --mode=link $(CCLD) $(AM_CFLAGS) $(CFLAGS) \
$(pressure_la_LDFLAGS) $(LDFLAGS) -o $@
stretching_energy_la_LIBADD =
-am_stretching_energy_la_OBJECTS = constant_area.lo
+am_stretching_energy_la_OBJECTS = stretching_energy.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) \
@@ -220,14 +227,15 @@
am__v_CCLD_0 = @echo " CCLD " $@;
am__v_CCLD_1 =
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) \
+ $(demoplugin_la_SOURCES) $(direct_force_on_c0_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) $(stretching_energy_la_SOURCES) \
+ $(direct_force_on_c0_la_SOURCES) $(nucleus_la_SOURCES) \
+ $(plane_confinement_la_SOURCES) $(pressure_la_SOURCES) \
+ $(stretching_energy_la_SOURCES) \
$(vmdefaulthardconstraints_la_SOURCES)
am__can_run_installinfo = \
case $$AM_UPDATE_INFO_DIR in \
@@ -377,7 +385,7 @@
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 stretching_energy.la
+lib_LTLIBRARIES = demoplugin.la vmdefaulthardconstraints.la nucleus.la plane_confinement.la pressure.la constant_volume.la constant_area.la stretching_energy.la direct_force_on_c0.la
demoplugin_la_SOURCES = demo_plugin.c
demoplugin_la_LDFLAGS = -module -avoid-version -export-dynamic
vmdefaulthardconstraints_la_SOURCES = default_hard_constraints.c
@@ -392,8 +400,10 @@
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_SOURCES = stretching_energy.c
stretching_energy_la_LDFLAGS = -module -avoid-version -export-dynamic
+direct_force_on_c0_la_SOURCES = direct_force_on_c0.c
+direct_force_on_c0_la_LDFLAGS = -module -avoid-version -export-dynamic
all: all-am
.SUFFIXES:
@@ -472,6 +482,9 @@
demoplugin.la: $(demoplugin_la_OBJECTS) $(demoplugin_la_DEPENDENCIES) $(EXTRA_demoplugin_la_DEPENDENCIES)
$(AM_V_CCLD)$(demoplugin_la_LINK) -rpath $(libdir) $(demoplugin_la_OBJECTS) $(demoplugin_la_LIBADD) $(LIBS)
+direct_force_on_c0.la: $(direct_force_on_c0_la_OBJECTS) $(direct_force_on_c0_la_DEPENDENCIES) $(EXTRA_direct_force_on_c0_la_DEPENDENCIES)
+ $(AM_V_CCLD)$(direct_force_on_c0_la_LINK) -rpath $(libdir) $(direct_force_on_c0_la_OBJECTS) $(direct_force_on_c0_la_LIBADD) $(LIBS)
+
nucleus.la: $(nucleus_la_OBJECTS) $(nucleus_la_DEPENDENCIES) $(EXTRA_nucleus_la_DEPENDENCIES)
$(AM_V_CCLD)$(nucleus_la_LINK) -rpath $(libdir) $(nucleus_la_OBJECTS) $(nucleus_la_LIBADD) $(LIBS)
@@ -497,9 +510,11 @@
include ./$(DEPDIR)/constant_volume.Plo
include ./$(DEPDIR)/default_hard_constraints.Plo
include ./$(DEPDIR)/demo_plugin.Plo
+include ./$(DEPDIR)/direct_force_on_c0.Plo
include ./$(DEPDIR)/nucleus.Plo
include ./$(DEPDIR)/plane_confinement.Plo
include ./$(DEPDIR)/pressure.Plo
+include ./$(DEPDIR)/stretching_energy.Plo
.c.o:
$(AM_V_CC)$(COMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ $<
diff --git a/src/plugins/Makefile.am b/src/plugins/Makefile.am
index dacef43..59af951 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 stretching_energy.la
+lib_LTLIBRARIES= demoplugin.la vmdefaulthardconstraints.la nucleus.la plane_confinement.la pressure.la constant_volume.la constant_area.la stretching_energy.la direct_force_on_c0.la
demoplugin_la_SOURCES= demo_plugin.c
demoplugin_la_LDFLAGS = -module -avoid-version -export-dynamic
@@ -21,7 +21,9 @@
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_SOURCES = stretching_energy.c
stretching_energy_la_LDFLAGS = -module -avoid-version -export-dynamic
+direct_force_on_c0_la_SOURCES = direct_force_on_c0.c
+direct_force_on_c0_la_LDFLAGS = -module -avoid-version -export-dynamic
diff --git a/src/plugins/Makefile.in b/src/plugins/Makefile.in
index d7fca36..cc92f88 100644
--- a/src/plugins/Makefile.in
+++ b/src/plugins/Makefile.in
@@ -151,6 +151,13 @@
demoplugin_la_LINK = $(LIBTOOL) $(AM_V_lt) --tag=CC $(AM_LIBTOOLFLAGS) \
$(LIBTOOLFLAGS) --mode=link $(CCLD) $(AM_CFLAGS) $(CFLAGS) \
$(demoplugin_la_LDFLAGS) $(LDFLAGS) -o $@
+direct_force_on_c0_la_LIBADD =
+am_direct_force_on_c0_la_OBJECTS = direct_force_on_c0.lo
+direct_force_on_c0_la_OBJECTS = $(am_direct_force_on_c0_la_OBJECTS)
+direct_force_on_c0_la_LINK = $(LIBTOOL) $(AM_V_lt) --tag=CC \
+ $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) --mode=link $(CCLD) \
+ $(AM_CFLAGS) $(CFLAGS) $(direct_force_on_c0_la_LDFLAGS) \
+ $(LDFLAGS) -o $@
nucleus_la_LIBADD =
am_nucleus_la_OBJECTS = nucleus.lo
nucleus_la_OBJECTS = $(am_nucleus_la_OBJECTS)
@@ -171,7 +178,7 @@
$(LIBTOOLFLAGS) --mode=link $(CCLD) $(AM_CFLAGS) $(CFLAGS) \
$(pressure_la_LDFLAGS) $(LDFLAGS) -o $@
stretching_energy_la_LIBADD =
-am_stretching_energy_la_OBJECTS = constant_area.lo
+am_stretching_energy_la_OBJECTS = stretching_energy.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) \
@@ -220,14 +227,15 @@
am__v_CCLD_0 = @echo " CCLD " $@;
am__v_CCLD_1 =
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) \
+ $(demoplugin_la_SOURCES) $(direct_force_on_c0_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) $(stretching_energy_la_SOURCES) \
+ $(direct_force_on_c0_la_SOURCES) $(nucleus_la_SOURCES) \
+ $(plane_confinement_la_SOURCES) $(pressure_la_SOURCES) \
+ $(stretching_energy_la_SOURCES) \
$(vmdefaulthardconstraints_la_SOURCES)
am__can_run_installinfo = \
case $$AM_UPDATE_INFO_DIR in \
@@ -377,7 +385,7 @@
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 stretching_energy.la
+lib_LTLIBRARIES = demoplugin.la vmdefaulthardconstraints.la nucleus.la plane_confinement.la pressure.la constant_volume.la constant_area.la stretching_energy.la direct_force_on_c0.la
demoplugin_la_SOURCES = demo_plugin.c
demoplugin_la_LDFLAGS = -module -avoid-version -export-dynamic
vmdefaulthardconstraints_la_SOURCES = default_hard_constraints.c
@@ -392,8 +400,10 @@
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_SOURCES = stretching_energy.c
stretching_energy_la_LDFLAGS = -module -avoid-version -export-dynamic
+direct_force_on_c0_la_SOURCES = direct_force_on_c0.c
+direct_force_on_c0_la_LDFLAGS = -module -avoid-version -export-dynamic
all: all-am
.SUFFIXES:
@@ -472,6 +482,9 @@
demoplugin.la: $(demoplugin_la_OBJECTS) $(demoplugin_la_DEPENDENCIES) $(EXTRA_demoplugin_la_DEPENDENCIES)
$(AM_V_CCLD)$(demoplugin_la_LINK) -rpath $(libdir) $(demoplugin_la_OBJECTS) $(demoplugin_la_LIBADD) $(LIBS)
+direct_force_on_c0.la: $(direct_force_on_c0_la_OBJECTS) $(direct_force_on_c0_la_DEPENDENCIES) $(EXTRA_direct_force_on_c0_la_DEPENDENCIES)
+ $(AM_V_CCLD)$(direct_force_on_c0_la_LINK) -rpath $(libdir) $(direct_force_on_c0_la_OBJECTS) $(direct_force_on_c0_la_LIBADD) $(LIBS)
+
nucleus.la: $(nucleus_la_OBJECTS) $(nucleus_la_DEPENDENCIES) $(EXTRA_nucleus_la_DEPENDENCIES)
$(AM_V_CCLD)$(nucleus_la_LINK) -rpath $(libdir) $(nucleus_la_OBJECTS) $(nucleus_la_LIBADD) $(LIBS)
@@ -497,9 +510,11 @@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/constant_volume.Plo@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/default_hard_constraints.Plo@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/demo_plugin.Plo@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/direct_force_on_c0.Plo@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/nucleus.Plo@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/plane_confinement.Plo@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/pressure.Plo@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/stretching_energy.Plo@am__quote@
.c.o:
@am__fastdepCC_TRUE@ $(AM_V_CC)$(COMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ $<
diff --git a/src/plugins/direct_force_on_c0.c b/src/plugins/direct_force_on_c0.c
new file mode 100644
index 0000000..94a1a7c
--- /dev/null
+++ b/src/plugins/direct_force_on_c0.c
@@ -0,0 +1,22 @@
+#include <stdlib.h>
+#include<math.h>
+
+#include "general.h"
+#include "energy.h"
+char plugin_name[] = "Direct force on curved proteins";
+char plugin_description[]= "Plugin for applying direct normal force on curved proteins (c0>0)";
+char plugin_author[] = "SAMO PENIC";
+
+
+ts_plugin_details *init (){
+ ts_plugin_details *details=(ts_plugin_details *)calloc(1,sizeof(ts_plugin_details));
+ details->name = plugin_name;
+ return details;
+}
+
+
+ts_double vm_energy_after_execute(ts_vesicle *vesicle, ts_vertex *vtx, ts_vertex *backup_vertices){
+ return direct_force_energy(vesicle,vtx,&backup_vertices[0]);
+}
+
+
diff --git a/src/plugins/stretching_energy.c b/src/plugins/stretching_energy.c
index fd44c52..2c537f4 100644
--- a/src/plugins/stretching_energy.c
+++ b/src/plugins/stretching_energy.c
@@ -2,10 +2,8 @@
#include<math.h>
#include "general.h"
-#include "vertex.h"
-#include "cell.h"
-#include "vesicle.h"
-#include "frame.h"
+#include "energy.h"
+
char plugin_name[] = "Stretching energy";
char plugin_description[]= "Plugin adds stretching energy to Monte Carlo steps";
char plugin_author[] = "SAMO PENIC";
@@ -58,8 +56,9 @@
stretchenergy(vesicle, vtx->tristar[i]);
data->dstretchenergy+=vtx->tristar[i]->energy;
}
+ return data->dstretchenergy;
}
- return data->dstretchenergy;
+ return 0.0;
}
diff --git a/src/vertexmove.c b/src/vertexmove.c
index 2b08dc8..362b895 100644
--- a/src/vertexmove.c
+++ b/src/vertexmove.c
@@ -20,7 +20,7 @@
ts_uint i;
ts_bool retval;
ts_uint cellidx;
- ts_double delta_energy, oenergy,dstretchenergy=0.0;
+ ts_double delta_energy, oenergy;
ts_double costheta,sintheta,phi,r;
//This will hold all the information of vtx and its neighbours
ts_vertex backupvtx[20]; // *constvol_vtx_moved=NULL, *constvol_vtx_backup=NULL;
@@ -62,12 +62,6 @@
}
/* End of vm_energy_before_prepare() */
- //stretching energy 1 of 3
- if(vesicle->tape->stretchswitch==1){
- for(i=0;i<vtx->tristar_no;i++) dstretchenergy-=vtx->tristar[i]->energy;
- }
- delta_energy=0;
-
//update the normals of triangles that share bead i.
for(i=0;i<vtx->tristar_no;i++) triangle_normal_vector(vtx->tristar[i]);
oenergy=vtx->energy;
@@ -80,7 +74,6 @@
delta_energy+=vtx->neigh[i]->xk*(vtx->neigh[i]->energy-oenergy);
}
-
/* Entry point for plugin vm_energy_after_execute() */
vesicle->plist->pointer=vesicle->plist->chain->vm_energy_after_execute;
@@ -88,21 +81,9 @@
delta_energy+=vesicle->plist->pointer->plugin->function->vm_energy_after_execute(vesicle, vtx, backupvtx);
vesicle->plist->pointer=vesicle->plist->pointer->next;
}
+/* End of vm_energy_after_execute() */
-/* Vertices with spontaneous curvature may have spontaneous force perpendicular to the surface of the vesicle. additional delta energy is calculated in this function */
- delta_energy+=direct_force_energy(vesicle,vtx,backupvtx);
-
- //stretching energy 2 of 3
- if(vesicle->tape->stretchswitch==1){
- for(i=0;i<vtx->tristar_no;i++){
- stretchenergy(vesicle, vtx->tristar[i]);
- dstretchenergy+=vtx->tristar[i]->energy;
- }
- }
-
- delta_energy+=dstretchenergy;
-
/* No poly-bond energy for now!
if(vtx->grafted_poly!=NULL){
delta_energy+=
@@ -153,14 +134,6 @@
//update the normals of triangles that share bead i.
for(i=0;i<vtx->tristar_no;i++) triangle_normal_vector(vtx->tristar[i]);
-
- //stretching energy 3 of 3
- if(vesicle->tape->stretchswitch==1){
- for(i=0;i<vtx->tristar_no;i++){
- stretchenergy(vesicle,vtx->tristar[i]);
- }
- }
-
/* Entry point for plugin vm_before_montecarlo_constraint() function */
--
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