WIP: modular library. Progress: added mesh_gen folder to define Gmsh-based mesh generation for particles; better organization of libraries; test/test_data/peridem/twop_circ/main.cpp implements twop_circ test without needing any input file. Our main goal is to minimize the complex input file preparation. We want to define the problem in a main.cpp file without less efforts. Everytime, we want to create a new simulation, we can either define main.cpp or reuse json file.

Author: prashjha

CMakeLists.txt

@@ -150,6 +150,10 @@ if(${Enable_Documentation})
     find_package(Doxygen)
 endif()
 
+# Add Gmsh
+find_package(Gmsh REQUIRED)
+include_directories(${GMSH_INCLUDE_DIRS})
+
 #----------------------------------#
 #<<<<<<<<<< Include directories >>>>>>>>>>#
 #----------------------------------#
@@ -167,17 +171,19 @@ include_directories(src)
 add_subdirectory(external/)
 
 # PeriDEM sub-directories
-add_subdirectory(src/util)
+add_subdirectory(src/fe)
+add_subdirectory(src/fracture)
 add_subdirectory(src/geom)
-add_subdirectory(src/rw)
 add_subdirectory(src/inp)
-add_subdirectory(src/material)
 add_subdirectory(src/loading)
-add_subdirectory(src/fracture)
-add_subdirectory(src/fe)
-add_subdirectory(src/particle)
-add_subdirectory(src/nsearch)
+add_subdirectory(src/material)
+add_subdirectory(src/mesh)
+add_subdirectory(src/mesh_gen)
 add_subdirectory(src/model)
+add_subdirectory(src/nsearch)
+add_subdirectory(src/particle)
+add_subdirectory(src/rw)
+add_subdirectory(src/util)
 
 # test directory
 if(${Enable_Tests})

apps/example-modular/main.cpp

@@ -216,15 +216,15 @@ int main(int argc, char *argv[]) {
   pGenJson["Data"]["N"] = 3; // three particles
 
   // p1
-  pGenJson["Data"]["0"] = {{"x", 0.}, {"y", 0.}, {"z", 0.}, {"o", 0.}, {"s", 1.},
+  pGenJson["Data"]["0"] = {{"x", 0.}, {"y", 0.}, {"z", 0.}, {"theta", 0.}, {"s", 1.},
                            {"geom_id", 0}, {"mat_id", 0}, {"contact_id", 0}};
 
   // p1
-  pGenJson["Data"]["1"] = {{"x", 0.}, {"y", 0.}, {"z", 0.}, {"o", 0.}, {"s", 1.},
+  pGenJson["Data"]["1"] = {{"x", 0.}, {"y", 0.}, {"z", 0.}, {"theta", 0.}, {"s", 1.},
                            {"geom_id", 1}, {"mat_id", 1}, {"contact_id", 1}};
 
   // p1
-  pGenJson["Data"]["2"] = {{"x", 0.}, {"y", 0.}, {"z", 0.}, {"o", 0.}, {"s", 1.},
+  pGenJson["Data"]["2"] = {{"x", 0.}, {"y", 0.}, {"z", 0.}, {"theta", 0.}, {"s", 1.},
                            {"geom_id", 2}, {"mat_id", 1}, {"contact_id", 1}};
 
   // add to json

apps/peridynamics/main.cpp

@@ -32,7 +32,7 @@
 #include "rw/vtkParticleWriter.h"
 #include "rw/vtkParticleReader.h"
 #include "fe/elemIncludes.h"
-#include "fe/meshUtil.h"
+#include "mesh/meshUtil.h"
 
 #include <format>
 #include <print>

apps/twoparticle_demo/main.cpp

@@ -28,7 +28,7 @@
 #include "rw/vtkParticleWriter.h"
 #include "rw/vtkParticleReader.h"
 #include "fe/elemIncludes.h"
-#include "fe/meshUtil.h"
+#include "mesh/meshUtil.h"
 
 #include <format>
 #include <fstream>

cmake/FindGmsh.cmake

@@ -0,0 +1,68 @@
+# -------------------------------------------
+# Copyright (c) 2021 - 2024 Prashant K. Jha
+# -------------------------------------------
+# PeriDEM https://github.com/prashjha/PeriDEM
+#
+# Distributed under the Boost Software License, Version 1.0. (See accompanying
+# file LICENSE)
+
+# Find Gmsh
+#
+# This sets the following variables:
+# GMSH_FOUND - True if Gmsh was found.
+# GMSH_INCLUDE_DIRS - Directories containing the Gmsh include files.
+# GMSH_LIBRARIES - Libraries needed to use Gmsh.
+# GMSH_VERSION - The version of Gmsh found.
+
+find_path(GMSH_INCLUDE_DIR
+    NAMES gmsh.h
+    PATHS
+        ${GMSH_DIR}/include
+        $ENV{GMSH_DIR}/include
+        /usr/include
+        /usr/local/include
+        /opt/local/include
+)
+
+find_library(GMSH_LIBRARY
+    NAMES gmsh libgmsh
+    PATHS
+        ${GMSH_DIR}/lib
+        ${GMSH_DIR}/lib64
+        $ENV{GMSH_DIR}/lib
+        $ENV{GMSH_DIR}/lib64
+        /usr/lib
+        /usr/lib64
+        /usr/local/lib
+        /usr/local/lib64
+        /opt/local/lib
+)
+
+# Try to find Gmsh version
+if(GMSH_INCLUDE_DIR AND EXISTS "${GMSH_INCLUDE_DIR}/gmsh.h")
+    file(STRINGS "${GMSH_INCLUDE_DIR}/gmsh.h" gmsh_version_str
+         REGEX "^#define[\t ]+GMSH_VERSION[\t ]+\".*\"")
+
+    string(REGEX REPLACE "^#define[\t ]+GMSH_VERSION[\t ]+\"([^\"]*)\".*" "\\1"
+           GMSH_VERSION "${gmsh_version_str}")
+    unset(gmsh_version_str)
+endif()
+
+include(FindPackageHandleStandardArgs)
+find_package_handle_standard_args(Gmsh
+    REQUIRED_VARS
+        GMSH_LIBRARY
+        GMSH_INCLUDE_DIR
+    VERSION_VAR
+        GMSH_VERSION
+)
+
+if(GMSH_FOUND)
+    set(GMSH_LIBRARIES ${GMSH_LIBRARY})
+    set(GMSH_INCLUDE_DIRS ${GMSH_INCLUDE_DIR})
+endif()
+
+mark_as_advanced(
+    GMSH_INCLUDE_DIR
+    GMSH_LIBRARY
+) 

src/fe/CMakeLists.txt

@@ -8,7 +8,8 @@
 
 AUX_SOURCE_DIRECTORY(./ SOURCES)
 
-add_library(FE ${SOURCES}
-        elemIncludes.h)
+add_library(FE ${SOURCES})
 
-target_link_libraries(FE PUBLIC Util RW ${METIS_LIB})
+target_link_libraries(FE PUBLIC
+        Util
+        Geom)

src/inp/input.h

@@ -26,7 +26,7 @@
  * *
  * Each deck is unique and is designed to initialize the higher level object
  * associated to it without needing information from other decks. For example,
- * fe::Mesh is initialized by inp::MeshDeck.
+ * mesh::Mesh is initialized by inp::MeshDeck.
  *
  * The namespace consists of Input and Policy member classes. Input class is
  * the main class responsible of reading input data into various decks.

src/loading/particleFLoading.cpp

@@ -47,7 +47,7 @@ void loading::ParticleFLoading::apply(const double &time,
       continue;
 
     // get bounding box (quite possibly be generic)
-    auto reg_box = bc.d_regionGeomData.d_geom_p->box();
+    auto reg_box = bc.d_regionGeomData.d_geom_p == nullptr ? std::pair<util::Point, util::Point>(util::Point(), util::Point()) : bc.d_regionGeomData.d_geom_p->box();
 
     // for (size_t i = 0; i < particle->getNumNodes(); i++) {
     tf::Executor executor(util::parallel::getNThreads());

src/loading/particleIC.cpp

@@ -28,7 +28,7 @@ void loading::applyIC(particle::BaseParticle *particle, const std::vector<inp::B
       continue;
 
     // get bounding box (quite possibly be generic)
-    auto reg_box = bc.d_regionGeomData.d_geom_p->box();
+    auto reg_box = bc.d_regionGeomData.d_geom_p == nullptr ? std::pair<util::Point, util::Point>(util::Point(), util::Point()) : bc.d_regionGeomData.d_geom_p->box();
 
     tf::Executor executor(util::parallel::getNThreads());
     tf::Taskflow taskflow;

src/loading/particleULoading.cpp

@@ -58,21 +58,16 @@ void loading::ParticleULoading::apply(const double &time,
     // get alias for bc data
     const auto &bc = d_bcData[s];
 
-    // if this is zero displacement condition, and if we have already applied
-    // displacement then do not need to reapply this
-    if (bc.d_isDisplacementZero && d_pZeroDisplacementApplied[s])
-      continue;
-
-    // set to true so that next time this is not called
+    // if this is zero displacement condition, we do not apply displacement
     if (bc.d_isDisplacementZero)
-      d_pZeroDisplacementApplied[s] = true;
+      continue;
 
     // check if we need to process this particle
     if (!needToProcessParticle(particle->getId(), bc))
       continue;
 
     // get bounding box (quite possibly be generic)
-    auto reg_box = bc.d_regionGeomData.d_geom_p->box();
+    auto reg_box = bc.d_regionGeomData.d_geom_p == nullptr ? std::pair<util::Point, util::Point>(util::Point(), util::Point()) : bc.d_regionGeomData.d_geom_p->box();
 
     // for (size_t i = 0; i < particle->getNumNodes(); i++) {
     tf::Executor executor(util::parallel::getNThreads());