| src/general.h | ●●●●● patch | view | raw | blame | history | |
| src/main.c | ●●●●● patch | view | raw | blame | history | |
| src/plugins/Makefile | ●●●●● patch | view | raw | blame | history | |
| src/plugins/Makefile.am | ●●●●● patch | view | raw | blame | history | |
| src/plugins/Makefile.in | ●●●●● patch | view | raw | blame | history | |
| src/plugins/default_hard_constraints.c | ●●●●● patch | view | raw | blame | history | |
| src/plugins/nucleus.c | ●●●●● patch | view | raw | blame | history | |
| src/plugins/plane_confinement.c | ●●●●● patch | view | raw | blame | history | |
| src/vertexmove.c | ●●●●● patch | view | raw | blame | history |
src/general.h
@@ -340,6 +340,7 @@ typedef struct { ts_plugin_chain *at_start; ts_plugin_chain *after_vesicle_init; ts_plugin_chain *vm_hard_constraint; ts_plugin_chain *cleanup; } ts_plugin_chains;
@@ -28,12 +28,15 @@ int main(int argv, char *argc[]){ 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)); strcpy(plugin0,"/home/samo/programiranje/trisurf-ng/src/plugins/.libs/demoplugin.so"); strcpy(plugin1,"/home/samo/programiranje/trisurf-ng/src/plugins/.libs/vmdefaulthardconstraints.so"); ts_char **plugins=(ts_char **)calloc(2,sizeof(ts_char *)); strcpy(plugin2,"/home/samo/programiranje/trisurf-ng/src/plugins/.libs/plane_confinement.so"); ts_char **plugins=(ts_char **)calloc(3,sizeof(ts_char *)); *plugins=plugin0; plugins[1]=plugin1; ts_plugin_list *plist=init_plugin_list(plugins,2); plugins[2]=plugin2; ts_plugin_list *plist=init_plugin_list(plugins,3); //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; src/plugins/Makefile
@@ -137,6 +137,19 @@ demoplugin_la_LINK = $(LIBTOOL) $(AM_V_lt) --tag=CC $(AM_LIBTOOLFLAGS) \ $(LIBTOOLFLAGS) --mode=link $(CCLD) $(AM_CFLAGS) $(CFLAGS) \ $(demoplugin_la_LDFLAGS) $(LDFLAGS) -o $@ nucleus_la_LIBADD = am_nucleus_la_OBJECTS = nucleus.lo nucleus_la_OBJECTS = $(am_nucleus_la_OBJECTS) nucleus_la_LINK = $(LIBTOOL) $(AM_V_lt) --tag=CC $(AM_LIBTOOLFLAGS) \ $(LIBTOOLFLAGS) --mode=link $(CCLD) $(AM_CFLAGS) $(CFLAGS) \ $(nucleus_la_LDFLAGS) $(LDFLAGS) -o $@ plane_confinement_la_LIBADD = am_plane_confinement_la_OBJECTS = plane_confinement.lo plane_confinement_la_OBJECTS = $(am_plane_confinement_la_OBJECTS) plane_confinement_la_LINK = $(LIBTOOL) $(AM_V_lt) --tag=CC \ $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) --mode=link $(CCLD) \ $(AM_CFLAGS) $(CFLAGS) $(plane_confinement_la_LDFLAGS) \ $(LDFLAGS) -o $@ vmdefaulthardconstraints_la_LIBADD = am_vmdefaulthardconstraints_la_OBJECTS = default_hard_constraints.lo vmdefaulthardconstraints_la_OBJECTS = \ @@ -179,9 +192,11 @@ am__v_CCLD_ = $(am__v_CCLD_$(AM_DEFAULT_VERBOSITY)) am__v_CCLD_0 = @echo " CCLD " $@; am__v_CCLD_1 = SOURCES = $(demoplugin_la_SOURCES) \ SOURCES = $(demoplugin_la_SOURCES) $(nucleus_la_SOURCES) \ $(plane_confinement_la_SOURCES) \ $(vmdefaulthardconstraints_la_SOURCES) DIST_SOURCES = $(demoplugin_la_SOURCES) \ DIST_SOURCES = $(demoplugin_la_SOURCES) $(nucleus_la_SOURCES) \ $(plane_confinement_la_SOURCES) \ $(vmdefaulthardconstraints_la_SOURCES) am__can_run_installinfo = \ case $$AM_UPDATE_INFO_DIR in \ @@ -331,11 +346,15 @@ top_builddir = ../.. top_srcdir = ../.. AM_CFLAGS = -Wall -Werror -DTS_VERSION=\"$(GITVERSION)\" -fgnu89-inline -Wno-error=date-time -I.. lib_LTLIBRARIES = demoplugin.la vmdefaulthardconstraints.la lib_LTLIBRARIES = demoplugin.la vmdefaulthardconstraints.la nucleus.la plane_confinement.la demoplugin_la_SOURCES = demo_plugin.c demoplugin_la_LDFLAGS = -module -avoid-version -export-dynamic vmdefaulthardconstraints_la_SOURCES = default_hard_constraints.c vmdefaulthardconstraints_la_LDFLAGS = -module -avoid-version -export-dynamic nucleus_la_SOURCES = nucleus.c nucleus_la_LDFLAGS = -module -avoid-version -export-dynamic plane_confinement_la_SOURCES = plane_confinement.c plane_confinement_la_LDFLAGS = -module -avoid-version -export-dynamic all: all-am .SUFFIXES: @@ -408,6 +427,12 @@ 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) 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) 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) 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) @@ -419,6 +444,8 @@ include ./$(DEPDIR)/default_hard_constraints.Plo include ./$(DEPDIR)/demo_plugin.Plo include ./$(DEPDIR)/nucleus.Plo include ./$(DEPDIR)/plane_confinement.Plo .c.o: $(AM_V_CC)$(COMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ $< src/plugins/Makefile.am
@@ -1,7 +1,14 @@ AM_CFLAGS = -Wall -Werror -DTS_VERSION=\"$(GITVERSION)\" -fgnu89-inline -Wno-error=date-time -I.. lib_LTLIBRARIES= demoplugin.la vmdefaulthardconstraints.la lib_LTLIBRARIES= demoplugin.la vmdefaulthardconstraints.la nucleus.la plane_confinement.la demoplugin_la_SOURCES= demo_plugin.c demoplugin_la_LDFLAGS = -module -avoid-version -export-dynamic vmdefaulthardconstraints_la_SOURCES = default_hard_constraints.c vmdefaulthardconstraints_la_LDFLAGS = -module -avoid-version -export-dynamic nucleus_la_SOURCES = nucleus.c nucleus_la_LDFLAGS = -module -avoid-version -export-dynamic plane_confinement_la_SOURCES = plane_confinement.c plane_confinement_la_LDFLAGS = -module -avoid-version -export-dynamic
@@ -137,6 +137,19 @@ demoplugin_la_LINK = $(LIBTOOL) $(AM_V_lt) --tag=CC $(AM_LIBTOOLFLAGS) \ $(LIBTOOLFLAGS) --mode=link $(CCLD) $(AM_CFLAGS) $(CFLAGS) \ $(demoplugin_la_LDFLAGS) $(LDFLAGS) -o $@ nucleus_la_LIBADD = am_nucleus_la_OBJECTS = nucleus.lo nucleus_la_OBJECTS = $(am_nucleus_la_OBJECTS) nucleus_la_LINK = $(LIBTOOL) $(AM_V_lt) --tag=CC $(AM_LIBTOOLFLAGS) \ $(LIBTOOLFLAGS) --mode=link $(CCLD) $(AM_CFLAGS) $(CFLAGS) \ $(nucleus_la_LDFLAGS) $(LDFLAGS) -o $@ plane_confinement_la_LIBADD = am_plane_confinement_la_OBJECTS = plane_confinement.lo plane_confinement_la_OBJECTS = $(am_plane_confinement_la_OBJECTS) plane_confinement_la_LINK = $(LIBTOOL) $(AM_V_lt) --tag=CC \ $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) --mode=link $(CCLD) \ $(AM_CFLAGS) $(CFLAGS) $(plane_confinement_la_LDFLAGS) \ $(LDFLAGS) -o $@ vmdefaulthardconstraints_la_LIBADD = am_vmdefaulthardconstraints_la_OBJECTS = default_hard_constraints.lo vmdefaulthardconstraints_la_OBJECTS = \ @@ -179,9 +192,11 @@ am__v_CCLD_ = $(am__v_CCLD_@AM_DEFAULT_V@) am__v_CCLD_0 = @echo " CCLD " $@; am__v_CCLD_1 = SOURCES = $(demoplugin_la_SOURCES) \ SOURCES = $(demoplugin_la_SOURCES) $(nucleus_la_SOURCES) \ $(plane_confinement_la_SOURCES) \ $(vmdefaulthardconstraints_la_SOURCES) DIST_SOURCES = $(demoplugin_la_SOURCES) \ DIST_SOURCES = $(demoplugin_la_SOURCES) $(nucleus_la_SOURCES) \ $(plane_confinement_la_SOURCES) \ $(vmdefaulthardconstraints_la_SOURCES) am__can_run_installinfo = \ case $$AM_UPDATE_INFO_DIR in \ @@ -331,11 +346,15 @@ 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 lib_LTLIBRARIES = demoplugin.la vmdefaulthardconstraints.la nucleus.la plane_confinement.la demoplugin_la_SOURCES = demo_plugin.c demoplugin_la_LDFLAGS = -module -avoid-version -export-dynamic vmdefaulthardconstraints_la_SOURCES = default_hard_constraints.c vmdefaulthardconstraints_la_LDFLAGS = -module -avoid-version -export-dynamic nucleus_la_SOURCES = nucleus.c nucleus_la_LDFLAGS = -module -avoid-version -export-dynamic plane_confinement_la_SOURCES = plane_confinement.c plane_confinement_la_LDFLAGS = -module -avoid-version -export-dynamic all: all-am .SUFFIXES: @@ -408,6 +427,12 @@ 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) 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) 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) 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) $(LIBS) @@ -419,6 +444,8 @@ @AMDEP_TRUE@@am__include@ @am__quote@./$(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)/nucleus.Plo@am__quote@ @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/plane_confinement.Plo@am__quote@ .c.o: @am__fastdepCC_TRUE@ $(AM_V_CC)$(COMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ $< src/plugins/default_hard_constraints.c
@@ -4,23 +4,13 @@ #include "vertex.h" #include "cell.h" char plugin_name[] = "Default hard constraints for vertex move"; char plugin_description[]= "Checks proximity with neighbors and with foreign vertices"; char plugin_description[]= "Checks proximity with neighbors, vertices in neighboring cells and with foreign vertices that may be in vicinity"; char plugin_author[] = "SAMO PENIC"; ts_plugin_details *init (){ // ts_fprintf(stdout,"Hello. Plugin %s is initiating. This will load the details section of the plugin\n", plugin_name); ts_plugin_details *details=(ts_plugin_details *)calloc(1,sizeof(ts_plugin_details)); details->name = plugin_name; return details; } void at_start(int argc, char **argv){ } void *after_vesicle_init(ts_vesicle *vesicle){ ts_fprintf(stdout,"Plugin \"%s\" is loaded.\n", plugin_name); return vesicle; } ts_bool vm_hard_constraint(ts_vesicle *vesicle, ts_vertex *vtx, ts_vertex *ovtx){ @@ -28,7 +18,6 @@ ts_uint cellidx; ts_double dist; ts_bool retval; //distance with neighbours check for(i=0;i<vtx->neigh_no;i++){ dist=vtx_distance_sq(vtx,vtx->neigh[i]); @@ -55,6 +44,3 @@ return TS_SUCCESS; } void cleanup(){ ts_fprintf(stdout,"Goodbye from plugin %s. This functions clears what would be created in init...\n",plugin_name); } src/plugins/nucleus.c
New file @@ -0,0 +1,33 @@ #include "plugins.h" #include <stdlib.h> #include "general.h" #include "vertex.h" #include "cell.h" char plugin_name[] = "Nucleus"; char plugin_description[]= "This plugin adds nucleus to the center of the vesicle. For now only vertexmove constraint is implemented."; 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_bool vm_hard_constraint(ts_vesicle *vesicle, ts_vertex *vtx, ts_vertex *ovtx){ // TODO: Maybe faster if checks only nucleus-neighboring cells // Nucleus penetration check: //#define SQ(x) x*x if(vesicle->R_nucleus>0.0){ 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){ return TS_FAIL; } } else if(vesicle->R_nucleusX>0.0){ 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){ return TS_FAIL; } } return TS_SUCCESS; }
New file @@ -0,0 +1,26 @@ #include <stdlib.h> #include "general.h" #include "vertex.h" #include "cell.h" char plugin_name[] = "Plane confimenent"; char plugin_description[]= "Confines vesicle between two planes d/2 above z=0 and d/2 below z=0. The plates squeeze vesicle with some predefined force."; 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_bool vm_hard_constraint(ts_vesicle *vesicle, ts_vertex *vtx, ts_vertex *ovtx){ // 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){ return TS_FAIL; } } return TS_SUCCESS; }
@@ -35,26 +35,6 @@ vtx->y=vtx->y+r*sintheta*sin(phi); vtx->z=vtx->z+r*costheta; // TODO: Maybe faster if checks only nucleus-neighboring cells // Nucleus penetration check: //#define SQ(x) x*x if(vesicle->R_nucleus>0.0){ 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 ((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; } } // 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){ @@ -62,18 +42,20 @@ return TS_FAIL; } } //#undef SQ /* Entry point for plugin vm_hard_constraint() function */ for(i=0; i<vesicle->plist->n;i++){ retval = vesicle->plist->plugin[i]->function->vm_hard_constraint(vesicle,vtx,&backupvtx[0]); ts_plugin_chain *ptr=vesicle->plist->chain->vm_hard_constraint; while(ptr!=NULL){ retval = ptr->plugin->function->vm_hard_constraint(vesicle,vtx, &backupvtx[0]); if(retval==TS_FAIL){ vtx=memcpy((void *)vtx,(void *)&backupvtx[0],sizeof(ts_vertex)); return TS_FAIL; } ptr=ptr->next; } //if all the tests are successful, then energy for vtx and neighbours is calculated for(i=0;i<vtx->neigh_no;i++){ memcpy((void *)&backupvtx[i+1],(void *)vtx->neigh[i],sizeof(ts_vertex));
