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Implement Laguerre-Voronoi tessellation #105

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2 changes: 2 additions & 0 deletions hdr/create.hpp
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Original file line number Diff line number Diff line change
Expand Up @@ -179,6 +179,8 @@ int create_crystal_structure(std::vector<cs::catom_t> &);

int voronoi_film(std::vector<cs::catom_t> &);

int voronoi_radical_film(std::vector<cs::catom_t> &);

void generate_multilayers(std::vector<cs::catom_t> & catom_array);

}
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11 changes: 11 additions & 0 deletions hdr/voronoi_radical.hpp
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@@ -0,0 +1,11 @@
#ifndef CREATE_VORONOI_RADICAL_H_
#define CREATE_VORONOI_RADICAL_H_
//==========================================================
// Namespace create_radical_voronoi
//==========================================================
namespace create_radical_voronoi{
extern bool rounded;
extern double voronoi_sd;/// Standard Deviation of voronoi grains
}

#endif //CREATE_VORONOI_RADICAL_H_
49 changes: 25 additions & 24 deletions makefile
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Expand Up @@ -29,8 +29,8 @@ MPIICC=mpiicpc -DMPICF
LIBS= -lstdc++
#-lm $(FFTLIBS) -L/opt/local/lib/

CCC_CFLAGS=-I./hdr -I./src/qvoronoi -O0
CCC_LDFLAGS=-I./hdr -I./src/qvoronoi -O0
CCC_CFLAGS=-I./hdr -I./src/qvoronoi -I./src/voro++ -O0
CCC_LDFLAGS=-I./hdr -I./src/qvoronoi -I./src/voro++ -O0

export LANG=C
export LC_ALL=C
Expand All @@ -40,41 +40,41 @@ export LC_ALL=C
CUDALIBS=-L/usr/local/cuda/lib64/ -lcuda -lcudart

# Debug Flags
ICC_DBCFLAGS= -O0 -C -I./hdr -I./src/qvoronoi
ICC_DBLFLAGS= -C -I./hdr -I./src/qvoronoi
ICC_DBCFLAGS= -O0 -C -I./hdr -I./src/qvoronoi -I./src/voro++
ICC_DBLFLAGS= -C -I./hdr -I./src/qvoronoi -I./src/voro++

GCC_DBCFLAGS= -g -pg -fprofile-arcs -ftest-coverage -Wall -Wextra -O0 -fbounds-check -pedantic -std=c++0x -Wno-long-long -I./hdr -I./src/qvoronoi -Wsign-compare
GCC_DBLFLAGS= -g -pg -fprofile-arcs -ftest-coverage -lstdc++ -std=c++0x -fbounds-check -I./hdr -I./src/qvoronoi -Wsign-compare
GCC_DBCFLAGS= -g -pg -fprofile-arcs -ftest-coverage -Wall -Wextra -O0 -fbounds-check -pedantic -std=c++0x -Wno-long-long -I./hdr -I./src/qvoronoi -I./src/voro++ -Wsign-compare
GCC_DBLFLAGS= -g -pg -fprofile-arcs -ftest-coverage -lstdc++ -std=c++0x -fbounds-check -I./hdr -I./src/qvoronoi -I./src/voro++ -Wsign-compare

PCC_DBCFLAGS= -O0 -I./hdr -I./src/qvoronoi
PCC_DBLFLAGS= -O0 -I./hdr -I./src/qvoronoi
IBM_DBCFLAGS= -O0 -Wall -pedantic -Wextra -I./hdr -I./src/qvoronoi
IBM_DBLFLAGS= -O0 -Wall -pedantic -Wextra -I./hdr -I./src/qvoronoi
PCC_DBCFLAGS= -O0 -I./hdr -I./src/qvoronoi -I./src/voro++
PCC_DBLFLAGS= -O0 -I./hdr -I./src/qvoronoi -I./src/voro++
IBM_DBCFLAGS= -O0 -Wall -pedantic -Wextra -I./hdr -I./src/qvoronoi -I./src/voro++
IBM_DBLFLAGS= -O0 -Wall -pedantic -Wextra -I./hdr -I./src/qvoronoi -I./src/voro++

LLVM_DBCFLAGS= -Wall -Wextra -O0 -pedantic -std=c++11 -Wno-long-long -I./hdr -I./src/qvoronoi -Wsign-compare
LLVM_DBLFLAGS= -Wall -Wextra -O0 -lstdc++ -I./hdr -I./src/qvoronoi -Wsign-compare
LLVM_DBCFLAGS= -Wall -Wextra -O0 -pedantic -std=c++11 -Wno-long-long -I./hdr -I./src/qvoronoi -I./src/voro++ -Wsign-compare
LLVM_DBLFLAGS= -Wall -Wextra -O0 -lstdc++ -I./hdr -I./src/qvoronoi -I./src/voro++ -Wsign-compare

# Performance Flags
ICC_CFLAGS= -O3 -axCORE-AVX2 -fno-alias -align -falign-functions -I./hdr -I./src/qvoronoi
ICC_LDFLAGS= -I./hdr -I./src/qvoronoi -axCORE-AVX2
ICC_CFLAGS= -O3 -axCORE-AVX2 -fno-alias -align -falign-functions -I./hdr -I./src/qvoronoi -I./src/voro++
ICC_LDFLAGS= -I./hdr -I./src/qvoronoi -I./src/voro++ -axCORE-AVX2
#ICC_CFLAGS= -O3 -xT -ipo -static -fno-alias -align -falign-functions -vec-report -I./hdr
#ICC_LDFLAGS= -lstdc++ -ipo -I./hdr -xT -vec-report

LLVM_CFLAGS= -Wall -pedantic -O3 -mtune=native -funroll-loops -I./hdr -I./src/qvoronoi
LLVM_LDFLAGS= -lstdc++ -I./hdr -I./src/qvoronoi
LLVM_CFLAGS= -Wall -pedantic -O3 -mtune=native -funroll-loops -I./hdr -I./src/qvoronoi -I./src/voro++
LLVM_LDFLAGS= -lstdc++ -I./hdr -I./src/qvoronoi -I./src/voro++

GCC_CFLAGS=-O3 -mtune=native -funroll-all-loops -fexpensive-optimizations -funroll-loops -I./hdr -I./src/qvoronoi -std=c++11 -Wsign-compare
GCC_LDFLAGS= -lstdc++ -I./hdr -I./src/qvoronoi -Wsign-compare
GCC_CFLAGS=-O3 -mtune=native -funroll-all-loops -fexpensive-optimizations -funroll-loops -I./hdr -I./src/qvoronoi -I./src/voro++ -std=c++11 -Wsign-compare
GCC_LDFLAGS= -lstdc++ -I./hdr -I./src/qvoronoi -I./src/voro++ -Wsign-compare

PCC_CFLAGS=-O2 -march=barcelona -ipa -I./hdr -I./src/qvoronoi
PCC_LDFLAGS= -I./hdr -I./src/qvoronoi -O2 -march=barcelona -ipa
PCC_CFLAGS=-O2 -march=barcelona -ipa -I./hdr -I./src/qvoronoi -I./src/voro++
PCC_LDFLAGS= -I./hdr -I./src/qvoronoi -I./src/voro++ -O2 -march=barcelona -ipa


IBM_CFLAGS=-O5 -qarch=450 -qtune=450 -I./hdr -I./src/qvoronoi
IBM_LDFLAGS= -lstdc++ -I./hdr -I./src/qvoronoi -O5 -qarch=450 -qtune=450
IBM_CFLAGS=-O5 -qarch=450 -qtune=450 -I./hdr -I./src/qvoronoi -I./src/voro++
IBM_LDFLAGS= -lstdc++ -I./hdr -I./src/qvoronoi -I./src/voro++ -O5 -qarch=450 -qtune=450

CRAY_CFLAGS= -O3 -hfp3 -I./hdr -I./src/qvoronoi
CRAY_LDFLAGS= -I./hdr -I./src/qvoronoi
CRAY_CFLAGS= -O3 -hfp3 -I./hdr -I./src/qvoronoi -I./src/voro++
CRAY_LDFLAGS= -I./hdr -I./src/qvoronoi -I./src/voro++


# Save git commit in simple function
Expand Down Expand Up @@ -153,6 +153,7 @@ include src/statistics/makefile
include src/unitcell/makefile
include src/vio/makefile
include src/environment/makefile
include src/voro++/makefile

# Cuda must be last for some odd reason
include src/cuda/makefile
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2 changes: 2 additions & 0 deletions src/create/data.cpp
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Expand Up @@ -44,6 +44,8 @@ namespace create{
double voronoi_grain_size = 50.0;
double voronoi_grain_spacing = 10.0;

double voronoi_tiny_grain_chance = 0.0;

double bubble_radius = 0.3333;
double bubble_nucleation_height = 0.0;

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16 changes: 16 additions & 0 deletions src/create/interface.cpp
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Expand Up @@ -14,6 +14,7 @@
#include "create.hpp"
#include "vio.hpp"
#include "voronoi.hpp"
#include "voronoi_radical.hpp"
#include "random.hpp"
// Internal sim header
#include "internal.hpp"
Expand Down Expand Up @@ -141,6 +142,11 @@ namespace create{
cs::system_creation_flags[2]=3;
return true;
}
test="laguerre-voronoi-film";
if(word==test){
cs::system_creation_flags[2]=5;
return true;
}
test="voronoi-grain-substructure";
if(word==test){
create::internal::generate_voronoi_substructure = true;
Expand All @@ -156,6 +162,7 @@ namespace create{
double vsd=atof(value.c_str());
vin::check_for_valid_value(vsd, word, line, prefix, unit, "none", 0.0, 1.0,"input","0.0 - 1.0");
create_voronoi::voronoi_sd=vsd;
create_radical_voronoi::voronoi_sd=vsd;
return true;
}
//--------------------------------------------------------------------
Expand All @@ -175,6 +182,7 @@ namespace create{
test="voronoi-rounded-grains";
if(word==test || word == "rounded-grains"){
create_voronoi::rounded=true;
create_radical_voronoi::rounded=true;
return true;
}
test="voronoi-include-boundary-grains";
Expand Down Expand Up @@ -444,6 +452,14 @@ namespace create{
return true;
}
//--------------------------------------------------------------------
test="voronoi-tiny-grain-chance";
if(word==test){
double tgchance=atof(value.c_str());
vin::check_for_valid_value(tgchance, word, line, prefix, unit, "none", 0.0, 1.0,"input","0.0 - 1.0");
create::internal::voronoi_tiny_grain_chance=tgchance;
return true;
}
//--------------------------------------------------------------------
test="cone";
if(word==test){
cs::system_creation_flags[1]=8;
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2 changes: 2 additions & 0 deletions src/create/internal.hpp
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Expand Up @@ -132,6 +132,8 @@ namespace create{
extern double voronoi_grain_size;
extern double voronoi_grain_spacing;

extern double voronoi_tiny_grain_chance;

extern double bubble_radius;
extern double bubble_nucleation_height;

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1 change: 1 addition & 0 deletions src/create/makefile
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Expand Up @@ -40,6 +40,7 @@ voronoi.o \
voronoi_grain_rounding.o \
voronoi_substructure.o \
voronoi_vertex_points.o \
voronoi_radical.o \
write_grain_vertices.o

# Append module objects to global tree
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4 changes: 4 additions & 0 deletions src/create/system_type.cpp
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Expand Up @@ -115,6 +115,10 @@ int create_system_type(std::vector<cs::catom_t> & catom_array){
err::vexit();
break;

case 5: // Radical Voronoi Granular Film
voronoi_radical_film(catom_array);
break;

default:{
std::cerr << "Unknown system type requested, exiting" << std::endl;
err::vexit();
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