From 36dba86649e71d2a56657320ddf98a1af2055023 Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@gmail.com>
Date: Thu, 28 Feb 2019 20:04:16 +0000
Subject: [PATCH] Some changes to plugins to allow storage of data. Pressure is a plugin now
---
src/plugins/.libs/demoplugin.a | 0
src/main.c | 7 +
src/plugins.c | 10 +++
src/plugins/Makefile.am | 5 +
src/plugins/.libs/demo_plugin.o | 0
src/plugins/Makefile | 18 +++++-
src/plugins/Makefile.in | 18 +++++-
src/plugins/demo_plugin.o | 0
src/plugins/pressure.c | 37 ++++++++++++
src/general.h | 6 +
src/vertexmove.c | 20 +++---
src/plugins/.libs/demoplugin.so | 0
12 files changed, 100 insertions(+), 21 deletions(-)
diff --git a/src/general.h b/src/general.h
index 16025f2..4e834ed 100644
--- a/src/general.h
+++ b/src/general.h
@@ -309,7 +309,7 @@
void (*at_start)(int argc, char **argv);
void *(*after_vesicle_init)(void *vesicle);
ts_bool (*vm_hard_constraint)(void *vesicle, ts_vertex *vtx, ts_vertex *odl_vtx);
- ts_double (*vm_energy_before_prepare)(void *vesicle, ts_vertex *vtx);
+ void (*vm_energy_before_prepare)(void *vesicle, ts_vertex *vtx);
ts_double (*vm_energy_before_execute)(void *vesicle, ts_vertex *vtx);
ts_double (*vm_energy_after_prepare)(void *vesicle, ts_vertex *vtx);
ts_double (*vm_energy_after_execute)(void *vesicle, ts_vertex *vtx);
@@ -322,6 +322,7 @@
ts_char *name;
ts_char *description;
ts_char *author;
+ void *data;
} ts_plugin_details;
typedef struct {
@@ -341,6 +342,8 @@
ts_plugin_chain *at_start;
ts_plugin_chain *after_vesicle_init;
ts_plugin_chain *vm_hard_constraint;
+ ts_plugin_chain *vm_energy_before_prepare;
+ ts_plugin_chain *vm_energy_after_execute;
ts_plugin_chain *cleanup;
} ts_plugin_chains;
@@ -349,6 +352,7 @@
ts_uint n;
ts_plugin **plugin;
ts_plugin_chains *chain;
+ ts_plugin_chain *pointer;
} ts_plugin_list;
/* end plugins */
diff --git a/src/main.c b/src/main.c
index 3cfc2af..6d19213 100644
--- a/src/main.c
+++ b/src/main.c
@@ -29,14 +29,17 @@
ts_char *plugin0 = (ts_char *)calloc(255,sizeof(ts_char));
ts_char *plugin1 = (ts_char *)calloc(255,sizeof(ts_char));
ts_char *plugin2 = (ts_char *)calloc(255,sizeof(ts_char));
+ ts_char *plugin3 = (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");
- ts_char **plugins=(ts_char **)calloc(3,sizeof(ts_char *));
+ strcpy(plugin3,"/home/samo/programiranje/trisurf-ng/src/plugins/.libs/pressure.so");
+ ts_char **plugins=(ts_char **)calloc(4,sizeof(ts_char *));
*plugins=plugin0;
plugins[1]=plugin1;
plugins[2]=plugin2;
- ts_plugin_list *plist=init_plugin_list(plugins,3);
+ plugins[3]=plugin3;
+ ts_plugin_list *plist=init_plugin_list(plugins,4);
//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.c b/src/plugins.c
index 84983aa..e94241f 100644
--- a/src/plugins.c
+++ b/src/plugins.c
@@ -155,9 +155,17 @@
if(plist->plugin[i]->function->at_start!=NULL){
plist->chain->at_start=plugin_to_chain(plist->chain->at_start, plist->plugin[i]);
}
+ if(plist->plugin[i]->function->vm_hard_constraint!=NULL){
+ plist->chain->vm_hard_constraint=plugin_to_chain(plist->chain->vm_hard_constraint, plist->plugin[i]);
+ }
+ if(plist->plugin[i]->function->vm_energy_before_prepare!=NULL){
+ plist->chain->vm_energy_before_prepare=plugin_to_chain(plist->chain->vm_energy_before_prepare, plist->plugin[i]);
+ }
+ if(plist->plugin[i]->function->vm_energy_after_execute!=NULL){
+ plist->chain->vm_energy_after_execute=plugin_to_chain(plist->chain->vm_energy_after_execute, plist->plugin[i]);
+ }
}
- //printf("%s", plist->chain->at_start->next->plugin->filename);
plist->n=number_of_plugins;
return plist;
}
diff --git a/src/plugins/.libs/demo_plugin.o b/src/plugins/.libs/demo_plugin.o
index e51de57..8706a04 100644
--- a/src/plugins/.libs/demo_plugin.o
+++ b/src/plugins/.libs/demo_plugin.o
Binary files differ
diff --git a/src/plugins/.libs/demoplugin.a b/src/plugins/.libs/demoplugin.a
index cf30305..0ce6a19 100644
--- a/src/plugins/.libs/demoplugin.a
+++ b/src/plugins/.libs/demoplugin.a
Binary files differ
diff --git a/src/plugins/.libs/demoplugin.so b/src/plugins/.libs/demoplugin.so
index 14ba685..b2316d0 100755
--- a/src/plugins/.libs/demoplugin.so
+++ b/src/plugins/.libs/demoplugin.so
Binary files differ
diff --git a/src/plugins/Makefile b/src/plugins/Makefile
index 3ff2734..08bbd37 100644
--- a/src/plugins/Makefile
+++ b/src/plugins/Makefile
@@ -150,6 +150,12 @@
$(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) --mode=link $(CCLD) \
$(AM_CFLAGS) $(CFLAGS) $(plane_confinement_la_LDFLAGS) \
$(LDFLAGS) -o $@
+pressure_la_LIBADD =
+am_pressure_la_OBJECTS = pressure.lo
+pressure_la_OBJECTS = $(am_pressure_la_OBJECTS)
+pressure_la_LINK = $(LIBTOOL) $(AM_V_lt) --tag=CC $(AM_LIBTOOLFLAGS) \
+ $(LIBTOOLFLAGS) --mode=link $(CCLD) $(AM_CFLAGS) $(CFLAGS) \
+ $(pressure_la_LDFLAGS) $(LDFLAGS) -o $@
vmdefaulthardconstraints_la_LIBADD =
am_vmdefaulthardconstraints_la_OBJECTS = default_hard_constraints.lo
vmdefaulthardconstraints_la_OBJECTS = \
@@ -193,10 +199,10 @@
am__v_CCLD_0 = @echo " CCLD " $@;
am__v_CCLD_1 =
SOURCES = $(demoplugin_la_SOURCES) $(nucleus_la_SOURCES) \
- $(plane_confinement_la_SOURCES) \
+ $(plane_confinement_la_SOURCES) $(pressure_la_SOURCES) \
$(vmdefaulthardconstraints_la_SOURCES)
DIST_SOURCES = $(demoplugin_la_SOURCES) $(nucleus_la_SOURCES) \
- $(plane_confinement_la_SOURCES) \
+ $(plane_confinement_la_SOURCES) $(pressure_la_SOURCES) \
$(vmdefaulthardconstraints_la_SOURCES)
am__can_run_installinfo = \
case $$AM_UPDATE_INFO_DIR in \
@@ -346,7 +352,7 @@
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
+lib_LTLIBRARIES = demoplugin.la vmdefaulthardconstraints.la nucleus.la plane_confinement.la pressure.la
demoplugin_la_SOURCES = demo_plugin.c
demoplugin_la_LDFLAGS = -module -avoid-version -export-dynamic
vmdefaulthardconstraints_la_SOURCES = default_hard_constraints.c
@@ -355,6 +361,8 @@
nucleus_la_LDFLAGS = -module -avoid-version -export-dynamic
plane_confinement_la_SOURCES = plane_confinement.c
plane_confinement_la_LDFLAGS = -module -avoid-version -export-dynamic
+pressure_la_SOURCES = pressure.c
+pressure_la_LDFLAGS = -module -avoid-version -export-dynamic
all: all-am
.SUFFIXES:
@@ -433,6 +441,9 @@
plane_confinement.la: $(plane_confinement_la_OBJECTS) $(plane_confinement_la_DEPENDENCIES) $(EXTRA_plane_confinement_la_DEPENDENCIES)
$(AM_V_CCLD)$(plane_confinement_la_LINK) -rpath $(libdir) $(plane_confinement_la_OBJECTS) $(plane_confinement_la_LIBADD) $(LIBS)
+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)
+
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)
@@ -446,6 +457,7 @@
include ./$(DEPDIR)/demo_plugin.Plo
include ./$(DEPDIR)/nucleus.Plo
include ./$(DEPDIR)/plane_confinement.Plo
+include ./$(DEPDIR)/pressure.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 c65261c..b28b8ff 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
+lib_LTLIBRARIES= demoplugin.la vmdefaulthardconstraints.la nucleus.la plane_confinement.la pressure.la
demoplugin_la_SOURCES= demo_plugin.c
demoplugin_la_LDFLAGS = -module -avoid-version -export-dynamic
@@ -12,3 +12,6 @@
plane_confinement_la_SOURCES = plane_confinement.c
plane_confinement_la_LDFLAGS = -module -avoid-version -export-dynamic
+pressure_la_SOURCES = pressure.c
+pressure_la_LDFLAGS = -module -avoid-version -export-dynamic
+
diff --git a/src/plugins/Makefile.in b/src/plugins/Makefile.in
index bf7b06d..8239434 100644
--- a/src/plugins/Makefile.in
+++ b/src/plugins/Makefile.in
@@ -150,6 +150,12 @@
$(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) --mode=link $(CCLD) \
$(AM_CFLAGS) $(CFLAGS) $(plane_confinement_la_LDFLAGS) \
$(LDFLAGS) -o $@
+pressure_la_LIBADD =
+am_pressure_la_OBJECTS = pressure.lo
+pressure_la_OBJECTS = $(am_pressure_la_OBJECTS)
+pressure_la_LINK = $(LIBTOOL) $(AM_V_lt) --tag=CC $(AM_LIBTOOLFLAGS) \
+ $(LIBTOOLFLAGS) --mode=link $(CCLD) $(AM_CFLAGS) $(CFLAGS) \
+ $(pressure_la_LDFLAGS) $(LDFLAGS) -o $@
vmdefaulthardconstraints_la_LIBADD =
am_vmdefaulthardconstraints_la_OBJECTS = default_hard_constraints.lo
vmdefaulthardconstraints_la_OBJECTS = \
@@ -193,10 +199,10 @@
am__v_CCLD_0 = @echo " CCLD " $@;
am__v_CCLD_1 =
SOURCES = $(demoplugin_la_SOURCES) $(nucleus_la_SOURCES) \
- $(plane_confinement_la_SOURCES) \
+ $(plane_confinement_la_SOURCES) $(pressure_la_SOURCES) \
$(vmdefaulthardconstraints_la_SOURCES)
DIST_SOURCES = $(demoplugin_la_SOURCES) $(nucleus_la_SOURCES) \
- $(plane_confinement_la_SOURCES) \
+ $(plane_confinement_la_SOURCES) $(pressure_la_SOURCES) \
$(vmdefaulthardconstraints_la_SOURCES)
am__can_run_installinfo = \
case $$AM_UPDATE_INFO_DIR in \
@@ -346,7 +352,7 @@
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
+lib_LTLIBRARIES = demoplugin.la vmdefaulthardconstraints.la nucleus.la plane_confinement.la pressure.la
demoplugin_la_SOURCES = demo_plugin.c
demoplugin_la_LDFLAGS = -module -avoid-version -export-dynamic
vmdefaulthardconstraints_la_SOURCES = default_hard_constraints.c
@@ -355,6 +361,8 @@
nucleus_la_LDFLAGS = -module -avoid-version -export-dynamic
plane_confinement_la_SOURCES = plane_confinement.c
plane_confinement_la_LDFLAGS = -module -avoid-version -export-dynamic
+pressure_la_SOURCES = pressure.c
+pressure_la_LDFLAGS = -module -avoid-version -export-dynamic
all: all-am
.SUFFIXES:
@@ -433,6 +441,9 @@
plane_confinement.la: $(plane_confinement_la_OBJECTS) $(plane_confinement_la_DEPENDENCIES) $(EXTRA_plane_confinement_la_DEPENDENCIES)
$(AM_V_CCLD)$(plane_confinement_la_LINK) -rpath $(libdir) $(plane_confinement_la_OBJECTS) $(plane_confinement_la_LIBADD) $(LIBS)
+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)
+
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) $(LIBS)
@@ -446,6 +457,7 @@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/demo_plugin.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@
.c.o:
@am__fastdepCC_TRUE@ $(AM_V_CC)$(COMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ $<
diff --git a/src/plugins/demo_plugin.o b/src/plugins/demo_plugin.o
index dbb066f..918e249 100644
--- a/src/plugins/demo_plugin.o
+++ b/src/plugins/demo_plugin.o
Binary files differ
diff --git a/src/plugins/pressure.c b/src/plugins/pressure.c
new file mode 100644
index 0000000..a79a438
--- /dev/null
+++ b/src/plugins/pressure.c
@@ -0,0 +1,37 @@
+#include <stdlib.h>
+#include "general.h"
+#include "vertex.h"
+#include "cell.h"
+char plugin_name[] = "Pressure";
+char plugin_description[]= "Defines extra energy term for relative pressure difference between the inner vesicle and outer vesicle";
+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;
+ details->data = (void *)calloc(1,sizeof(ts_double));
+ return details;
+}
+
+void vm_energy_before_prepare(ts_vesicle *vesicle, ts_vertex *vtx){
+ if(vesicle->pswitch == 1){
+ ts_double *dvol=(ts_double *)vesicle->plist->pointer->plugin->details->data;
+ ts_uint i;
+ //printf ("DVOL was %f\n", *dvol);
+ *dvol=0;
+ for(i=0;i<vtx->tristar_no;i++) *dvol-=vtx->tristar[i]->volume;
+ //printf ("DVOL is %f\n", *dvol);
+
+ }
+}
+
+ts_double vm_energy_after_execute(ts_vesicle *vesicle, ts_vertex *vtx){
+ ts_double delta_energy=0;
+ if(vesicle->pswitch == 1){
+ ts_double *dvol=(ts_double *)vesicle->plist->pointer->plugin->details->data;
+ ts_uint i;
+ for(i=0;i<vtx->tristar_no;i++) *dvol+=vtx->tristar[i]->volume;
+ delta_energy=-vesicle->pressure*(*dvol);
+ }
+ return delta_energy;
+}
diff --git a/src/vertexmove.c b/src/vertexmove.c
index c512ccd..0c08aff 100644
--- a/src/vertexmove.c
+++ b/src/vertexmove.c
@@ -35,13 +35,6 @@
vtx->y=vtx->y+r*sintheta*sin(phi);
vtx->z=vtx->z+r*costheta;
-// plane confinement check whether the new position of vertex will be out of bounds
- if(vesicle->tape->plane_confinement_switch){
- if(vtx->z>vesicle->confinement_plane.z_max || vtx->z<vesicle->confinement_plane.z_min){
- vtx=memcpy((void *)vtx,(void *)&backupvtx[0],sizeof(ts_vertex));
- return TS_FAIL;
- }
- }
/* Entry point for plugin vm_hard_constraint() function */
ts_plugin_chain *ptr=vesicle->plist->chain->vm_hard_constraint;
@@ -53,14 +46,21 @@
}
ptr=ptr->next;
}
+/* End of vm_hard_constraint() */
-
-
-//if all the tests are successful, then energy for vtx and neighbours is calculated
+/* Backuping the neighbours */
for(i=0;i<vtx->neigh_no;i++){
memcpy((void *)&backupvtx[i+1],(void *)vtx->neigh[i],sizeof(ts_vertex));
}
+/* Entry point for plugin vm_energy_before_prepare() */
+
+ vesicle->plist->pointer=vesicle->plist->chain->vm_energy_before_prepare;
+ while(vesicle->plist->pointer!=NULL){
+ vesicle->plist->pointer->plugin->function->vm_energy_before_prepare(vesicle, vtx);
+ vesicle->plist->pointer=vesicle->plist->pointer->next;
+ }
+/* Calculate energy for vtx and neighbours */
if(vesicle->pswitch == 1 || vesicle->tape->constvolswitch>0){
for(i=0;i<vtx->tristar_no;i++) dvol-=vtx->tristar[i]->volume;
}
--
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