diff --git a/OPIMaker.cpp b/OPIMaker.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..e7c56f39f18958163811ef4ab6db9853443a9400
--- /dev/null
+++ b/OPIMaker.cpp
@@ -0,0 +1,64 @@
+
+#include <iostream>
+#include <fstream>
+#include <sstream>
+#include <string>
+#include <algorithm>
+#include <map>
+
+
+int main(int argc, char *argv[])
+{
+ std::fstream opiin;
+ std::fstream opiout;
+ std::fstream input;
+ opiin.open (argv[1], std::fstream::in);
+ input.open (argv[2], std::fstream::in);
+ opiout.open (argv[3], std::fstream::out | std::fstream::trunc);
+ std::map<std::string,std::string> replacement_values;
+ std::string line;
+ while (std::getline(input, line))
+ {
+ std::istringstream ss(line);
+ std::string s = ss.str();
+ std::replace(s.begin(), s.end(), '-', ' ');
+ std::replace(s.begin(), s.end(), ':', ' ');
+ ss.str(s);
+
+ std::string name;
+ std::string value;
+
+ ss >> name >> value;
+ std::cout << name << value << std::endl << std::endl;
+ replacement_values[name] = value;
+ }
+ while(std::getline(opiin,line))
+ {
+ std::string name;
+ std::string value;
+ bool found = false;
+ for (auto it = replacement_values.begin(); it != replacement_values.end(); ++it)
+ {
+ std::string _token_str = "$" + it->first + " ";
+ size_t _pos = line.find(_token_str);
+ if ( std::string::npos != _pos && !found)
+ {
+ name = _token_str;
+ value = it->second;
+ found = true;
+ }
+ }
+ if (found)
+ {
+ opiout << name << " : " << value << std::endl;
+ }
+ else
+ {
+ opiout << line << std::endl;
+ }
+ }
+ opiin.close();
+ opiout.close();
+ input.close();
+}
+
diff --git a/OpenPhase.ipynb b/OpenPhase.ipynb
index dcabdb665170c68d6c7d80ceeee6f98eee30ec80..89592a5da0fb22c550e0c4acd0a9d16a2882e743 100644
--- a/OpenPhase.ipynb
+++ b/OpenPhase.ipynb
@@ -2,7 +2,7 @@
"cells": [
{
"cell_type": "code",
- "execution_count": null,
+ "execution_count": 67,
"id": "67dd6769",
"metadata": {},
"outputs": [
@@ -10,8 +10,55 @@
"name": "stdout",
"output_type": "stream",
"text": [
- "The job Martensite was saved and received the ID: 92\n"
+ "The job Martensite was saved and received the ID: 92\n",
+ "Output collection not implement yet.\n"
]
+ },
+ {
+ "data": {
+ "text/html": [
+ "<div>\n",
+ "<style scoped>\n",
+ " .dataframe tbody tr th:only-of-type {\n",
+ " vertical-align: middle;\n",
+ " }\n",
+ "\n",
+ " .dataframe tbody tr th {\n",
+ " vertical-align: top;\n",
+ " }\n",
+ "\n",
+ " .dataframe thead th {\n",
+ " text-align: right;\n",
+ " }\n",
+ "</style>\n",
+ "<table border=\"1\" class=\"dataframe\">\n",
+ " <thead>\n",
+ " <tr style=\"text-align: right;\">\n",
+ " <th></th>\n",
+ " <th>time</th>\n",
+ " <th>austenite</th>\n",
+ " <th>martensite</th>\n",
+ " </tr>\n",
+ " </thead>\n",
+ " <tbody>\n",
+ " <tr>\n",
+ " <th>0</th>\n",
+ " <td>0.0</td>\n",
+ " <td>100.0</td>\n",
+ " <td>0.0</td>\n",
+ " </tr>\n",
+ " </tbody>\n",
+ "</table>\n",
+ "</div>"
+ ],
+ "text/plain": [
+ " time austenite martensite\n",
+ "0 0.0 100.0 0.0"
+ ]
+ },
+ "execution_count": 67,
+ "metadata": {},
+ "output_type": "execute_result"
}
],
"source": [
@@ -26,17 +73,35 @@
"\n",
"class OpenPhase_RTC:\n",
" def __init__(self):\n",
- " self.input = GenericParameters(table_name=\"input\")\n",
- " self._dt = 1e-6\n",
+ " self.input = DataContainer(table_name=\"input\")\n",
+ " self._dt = 1\n",
+ " self._timesteps = 1\n",
+ " self._openmp = 1\n",
" self._path = None\n",
"\n",
" @property\n",
- " def value(self):\n",
+ " def dt(self):\n",
" return self._dt\n",
"\n",
- " @value.setter\n",
- " def value(self, dt):\n",
+ " @dt.setter\n",
+ " def dt(self, dt):\n",
" self._dt = dt\n",
+ " \n",
+ " @property\n",
+ " def timesteps(self):\n",
+ " return self._timesteps\n",
+ "\n",
+ " @timesteps.setter\n",
+ " def timesteps(self, timesteps):\n",
+ " self._timesteps = timesteps \n",
+ " \n",
+ " @property\n",
+ " def openmp(self):\n",
+ " return self._openmp\n",
+ "\n",
+ " @openmp.setter\n",
+ " def openmp(self, openmp):\n",
+ " self._openmp = openmp \n",
"\n",
" def read(self, path, wrap=True):\n",
" self._dt = self._dt.read(file_name=path, wrap=wrap)\n",
@@ -45,19 +110,66 @@
" def config_material(self):\n",
" pass\n",
"\n",
- " def write(self,path):\n",
+ " def getdata(self):\n",
" self.input['dt'] = self._dt\n",
- " self.input.write_file( \n",
- " file_name=\"input\",\n",
- " cwd=path\n",
- " )\n",
+ " self.input['nSteps'] = self._timesteps\n",
+ " self.input['nOMP'] = self._openmp\n",
+ " return self.input\n",
+ " \n",
+ "class OpenPhase_Grid:\n",
+ " def __init__(self):\n",
+ " self.input = DataContainer(table_name=\"input\")\n",
+ " self._dx = 1\n",
+ " self._SizeX = 1\n",
+ " self._SizeY = 1\n",
+ " self._SizeZ = 1\n",
+ " self._path = None\n",
+ "\n",
+ " @property\n",
+ " def SizeX(self):\n",
+ " return self._SizeX\n",
+ "\n",
+ " @SizeX.setter\n",
+ " def SizeX(self, SizeX):\n",
+ " self._SizeX = SizeX\n",
+ " \n",
+ " @property\n",
+ " def SizeY(self):\n",
+ " return self._SizeY\n",
+ "\n",
+ " @SizeY.setter\n",
+ " def SizeY(self, SizeY):\n",
+ " self._SizeY = SizeY \n",
+ " \n",
+ " @property\n",
+ " def SizeZ(self):\n",
+ " return self._SizeZ\n",
+ "\n",
+ " @SizeX.setter\n",
+ " def SizeZ(self, SizeZ):\n",
+ " self._SizeZ = SizeZ\n",
+ " \n",
+ " def read(self, path, wrap=True):\n",
+ " self._dx = self._dt.read(file_name=path, wrap=wrap)\n",
+ " self._path = path\n",
+ "\n",
+ " def config_material(self):\n",
+ " pass\n",
+ "\n",
+ " def getdata(self):\n",
+ " self.input['dx'] = self._dx\n",
+ " self.input['Nx'] = self._SizeX\n",
+ " self.input['Ny'] = self._SizeY\n",
+ " self.input['Nz'] = self._SizeZ\n",
+ " return self.input\n",
" \n",
"class OpenPhase(GenericJob):\n",
" def __init__(self, project, job_name):\n",
" super().__init__(project, job_name) \n",
- " #self.input = GenericParameters(table_name=\"input\")\n",
- " self.executable = \"/home/marvin/pyiron/projects/OpenPhase.sh input > output\"\n",
+ " self.input = DataContainer(table_name=\"input\")\n",
+ " self.executable = Martensite.working_directory + \"/../../../OpenPhase.sh input.yml > output\"\n",
" self._RTC = OpenPhase_RTC() \n",
+ " self._Grid = OpenPhase_Grid() \n",
" \n",
" @property\n",
" def RTC(self):\n",
@@ -65,10 +177,21 @@
"\n",
" @RTC.setter\n",
" def RTC(self, value):\n",
- " self._RTC = value \n",
+ " self._RTC = value \n",
+ " \n",
+ " @property\n",
+ " def Grid(self):\n",
+ " return self._Grid\n",
+ "\n",
+ " @Grid.setter\n",
+ " def Grid(self, value):\n",
+ " self._Grid = value \n",
" \n",
" def write_input(self): \n",
- " self._RTC.write(self.working_directory)\n",
+ " self.input.clear()\n",
+ " self.input.append(self._RTC.getdata())\n",
+ " self.input.append(self._Grid.getdata())\n",
+ " self.input.write(Martensite.working_directory + \"/input.yml\")\n",
"\n",
" def collect_output(self):\n",
" print(\"Output collection not implement yet.\")\n",
@@ -91,11 +214,19 @@
" \n",
"from pyiron import Project\n",
"qRTC = OpenPhase_RTC()\n",
+ "qRTC.dt = 1e-4\n",
+ "qRTC.timesteps = 100\n",
+ "qGrid = OpenPhase_Grid()\n",
+ "qGrid.dx = 1e-6\n",
+ "qGrid.SizeX = 100\n",
+ "qGrid.SizeY = 1\n",
+ "qGrid.SizeZ = 100\n",
"pr = Project(path='Martensite')\n",
"Martensite = pr.create_job(OpenPhase, 'Martensite',delete_existing_job=True)\n",
"Martensite.RTC = qRTC\n",
+ "Martensite.Grid = qGrid\n",
"Martensite.run()\n",
- "csv_file = \"/home/marvin/pyiron/projects/OpenPhase/output_Results/TextData/Volumes.opd\"\n",
+ "csv_file = Martensite.working_directory + \"/../../../OpenPhase/output_Results/TextData/Volumes.opd\"\n",
"\n",
"# Read csv file into dataframe\n",
"df = pd.read_csv(csv_file, names=['time','austenite','martensite'], skiprows=[0],delimiter=\" \",engine='python')\n",
diff --git a/OpenPhase.sh b/OpenPhase.sh
new file mode 100755
index 0000000000000000000000000000000000000000..afa1edd5f759e56d75b237d21bb874885dd500bc
--- /dev/null
+++ b/OpenPhase.sh
@@ -0,0 +1,4 @@
+#!/bin/bash
+/home/marvin/pyiron/projects/OpenPhase/OPIMaker /home/marvin/pyiron/projects/OpenPhase/preset_Martensite.opi $1 /home/marvin/pyiron/projects/OpenPhase/output
+/home/marvin/pyiron/projects/OpenPhase/Studio.exe /home/marvin/pyiron/projects/OpenPhase/output
+exit 0
diff --git a/preset_Martensite.opi b/preset_Martensite.opi
new file mode 100644
index 0000000000000000000000000000000000000000..c5c2ee28176f1b6d9a7b4830cdb8eac5cce7545a
--- /dev/null
+++ b/preset_Martensite.opi
@@ -0,0 +1,337 @@
+@Description
+
+$Description :
+Key modules
+Elasticity
+
+This preset illustrates martensitic transformation.
+
+@Initialization
+
+$InitType Initialization Type: Single
+$Rotation Rotation mode of initialization: none
+$PhaseIndex Phase: 0
+$Variant Symmetry Variant: -1
+
+
+@Modules
+
+$PhaseField PhaseField selected: Yes
+$Chemistry Chemistry selected: No
+$VacancyDiffusion VacancyDiffusion selected: No
+$ThermodynamicModel Thermodynamic model: None
+$IntfAnisotropy Interface anisotropy Cubic/Hex: $Nucleation Nucleation selected: Yes
+$Mechanics Mechanics selected: Yes
+$Plasticity Plasticity model: No
+$Damage Damage selected: No
+$HeatDiffusion HeatDiffusion selected: No
+$Flow Flow selected: No
+$UserDrivingForce UserDrivingForce selected: Yes
+$1Dsimulation Dedicated 1D output :No
+
+
+@Composition
+
+$DiffusionModel Diffusion model: None
+$RefElement_0 Name of reference element phase 0: FE
+$RefElement_1 Name of reference element phase 1: FE
+$State_0 State of phase 0: Solid
+$State_1 State of phase 1: Solid
+$Cmin_0_FE Minimum mole fractions: 0.0
+$Cmin_1_FE Minimum mole fractions: 0.0
+$Cmax_0_FE Maximum mole fractions: 1.0
+$Cmax_1_FE Maximum mole fractions: 1.0
+
+
+@BoundaryConditions
+
+$BC0X X axis boundary condition: Periodic
+$BCNX X axis far end boundary condition: Periodic
+$BC0Y Y axis boundary condition: Periodic
+$BCNY Y axis far end boundary condition: Periodic
+$BC0Z Z axis boundary condition: Periodic
+$BCNZ Z axis far end boundary condition: Periodic
+
+
+
+
+
+@DrivingForce
+
+$Average Driving force averaging: Yes
+$CutOff Driving force cutoff: 0.95
+$NoiseMode Noise: Zero
+$Noise_0_0 Noise Intensity: 0.0
+$Noise_0_1 Noise Intensity: 0.0
+$Noise_1_1 Noise Intensity: 0.0
+$Stabilization Phase-field stabilization enabled: No
+
+
+
+
+
+@ElasticProperties
+
+$StrainAccuracy Strain Accuracy: 1.0e-6
+$MAXIterations Maximum Iterations: 100
+$EModel Elasticity Model: KHACHATURYAN
+$SMODE Strain Mode: GREENLAGRANGE
+$BCX Boundary Conditions X: FreeBoundaries
+$BCY Boundary Conditions Y: FreeBoundaries
+$BCZ Boundary Conditions Z: FreeBoundaries
+$BCXY Boundary Conditions XY: FreeBoundaries
+$BCYZ Boundary Conditions YZ: FreeBoundaries
+$BCXZ Boundary Conditions XZ: FreeBoundaries
+$BCValueX BC Value X: 0
+$BCValueY BC Value Y: 0
+$BCValueZ BC Value Z: 0
+$BCValueXY BC Value XY: 0
+$BCValueYZ BC Value YZ: 0
+$BCValueXZ BC Value XZ: 0
+$Restrict Restrict: ASPECTRATIO
+$ElasticConstantMode Elastic Constant Mode: TENSOR
+$C_0 :
+237e9 117e9 117e9 0 0 0
+117e9 237e9 117e9 0 0 0
+117e9 117e9 237e9 0 0 0
+0 0 0 60e9 0 0
+0 0 0 0 60e9 0
+0 0 0 0 0 60e9
+
+$C_1 :
+1.87455e+11 1.11165e+11 1.06547e+11 9.20007e+08 1.90713e+10 -6.01830e+09
+1.11165e+11 1.81999e+11 1.11072e+11 7.61985e+09 -5.13189e+08 7.62600e+09
+1.06547e+11 1.11072e+11 2.26978e+11 -5.44643e+09 -1.16758e+10 -1.08325e+09
+9.20007e+08 7.61985e+09 -5.44643e+09 9.27720e+10 -1.08325e+09 -5.13193e+08
+1.90713e+10 -5.13189e+08 -1.16758e+10 -1.08325e+09 8.82470e+10 9.20007e+08
+-6.01830e+09 7.62600e+09 -1.08325e+09 -5.13193e+08 9.20007e+08 9.28654e+10
+
+$K_0 Bulk modulus: 0
+$K_1 Bulk modulus: 0
+$E_0 Young's modulus: 0
+$E_1 Young's modulus: 0
+$L_0 First Lame: 0
+$L_1 First Lame: 0
+$G_0 Shear modulus: 0
+$G_1 Shear modulus: 0
+$Nu_0 Poisson's ratio: 0
+$Nu_1 Poisson's ratio: 0
+$M_0 P-wave modulus: 0
+$M_1 P-wave modulus: 0
+$U_0 :
+1.0 0.0 0.0
+0.0 1.0 0.0
+0.0 0.0 1.0
+
+$U_1 :
+1.1137500 -0.0734422 0.132834
+0.0599654 1.1272300 0.059707
+-0.1933730 -0.0734419 0.783581
+
+$ConsiderExternalForces Consider External Forces: No
+$ChemoMechanicalCoupling Chemo-Mechanical coupling: No
+$Cref_0_FE Reference concentration: 0.0
+$Cref_1_FE Reference concentration: 0.0
+$Kappa_0_FE :
+0 0 0 0 0 0
+0 0 0 0 0 0
+0 0 0 0 0 0
+0 0 0 0 0 0
+0 0 0 0 0 0
+0 0 0 0 0 0
+
+$Kappa_1_FE :
+0 0 0 0 0 0
+0 0 0 0 0 0
+0 0 0 0 0 0
+0 0 0 0 0 0
+0 0 0 0 0 0
+0 0 0 0 0 0
+
+$Lambda_0_FE :
+0 0 0
+0 0 0
+0 0 0
+
+$Lambda_1_FE :
+0 0 0
+0 0 0
+0 0 0
+
+$ThermoMechanicalCoupling Thermo-Mechanical coupling: No
+$Tref_0 Reference temperature: 0.0
+$Tref_1 Reference temperature: 0.0
+$Gamma_0 :
+0 0 0 0 0 0
+0 0 0 0 0 0
+0 0 0 0 0 0
+0 0 0 0 0 0
+0 0 0 0 0 0
+0 0 0 0 0 0
+
+$Gamma_1 :
+0 0 0 0 0 0
+0 0 0 0 0 0
+0 0 0 0 0 0
+0 0 0 0 0 0
+0 0 0 0 0 0
+0 0 0 0 0 0
+
+$Alpha_0 :
+0 0 0
+0 0 0
+0 0 0
+
+$Alpha_1 :
+0 0 0
+0 0 0
+0 0 0
+
+$NeuberCorrection_0 Neuber correction: Yes
+$NeuberCorrection_1 Neuber correction: Yes
+$YoungsModulus_0 Neuber Young's modulus: 160e9
+$YoungsModulus_1 Neuber Young's modulus: 200e9
+$YieldStrength_0 Neuber Yield strength: 156e6
+$YieldStrength_1 Neuber Yield strength: 900e6
+$Hardening_0 Neuber hardening: 7
+$Hardening_1 Neuber hardening: 7
+
+
+
+
+
+@InterfaceProperties
+
+$EnergyModel_0_0 Stiffness Model: ISO
+$EnergyModel_0_1 Stiffness Model: ISO
+$EnergyModel_1_1 Stiffness Model: ISO
+$Sigma_0_0 Interface energy: 0.5
+$Sigma_0_1 Interface energy: 0.5
+$Sigma_1_1 Interface energy: 0.5
+$MobilityModel_0_0 Mobility Model: ISO
+$MobilityModel_0_1 Mobility Model: ISO
+$MobilityModel_1_1 Mobility Model: ISO
+$Mu_0_0 Interface mobility: 1.0e-13
+$Mu_0_1 Interface mobility: 1.0e-13
+$Mu_1_1 Interface mobility: 1.0e-13
+$Q_0_0 Activation energy: 0.0
+$Q_0_1 Activation energy: 0.0
+$Q_1_1 Activation energy: 0.0
+
+
+
+
+
+@Nucleation
+
+$Allowed_0_0 Nucleation of nucleating phase in matrix phase: No
+$Allowed_0_1 Nucleation of nucleating phase in matrix phase: No
+$Allowed_1_0 Nucleation of nucleating phase in matrix phase: Yes
+$Allowed_1_1 Nucleation of nucleating phase in matrix phase: No
+$Density_0_0 Particle density: 2.0e14
+$Density_0_1 Particle density: 2.0e14
+$Density_1_0 Particle density: 0.75e+18
+$Density_1_1 Particle density: 2.0e14
+$Tmin_0_0 Minimum temperature: 0.0
+$Tmin_0_1 Minimum temperature: 0.0
+$Tmin_1_0 Minimum temperature: 0
+$Tmin_1_1 Minimum temperature: 0.0
+$Tmax_0_0 Maximum temperature: 10000.0
+$Tmax_0_1 Maximum temperature: 10000.0
+$Tmax_1_0 Maximum temperature: 1000
+$Tmax_1_1 Maximum temperature: 10000.0
+$Orientation_0_0 Grain orientation mode: Parent
+$Orientation_0_1 Grain orientation mode: Parent
+$Orientation_1_0 Grain orientation mode: Parent
+$Orientation_1_1 Grain orientation mode: Parent
+$MobilityReduction Mobility reduction for nucleus stability: 1.0
+$Shielding_0_0 Minimum distance between nuclei: 10.0
+$Shielding_0_1 Minimum distance between nuclei: 10.0
+$Shielding_1_0 Minimum distance between nuclei: 10.0
+$Shielding_1_1 Minimum distance between nuclei: 10.0
+$RelDensity_0_0 Nucleation density relative to phase volume: Yes
+$RelDensity_0_1 Nucleation density relative to phase volume: Yes
+$RelDensity_1_0 Nucleation density relative to phase volume: Yes
+$RelDensity_1_1 Nucleation density relative to phase volume: Yes
+$NucleateEvery Nucleation interval in timesteps: 1
+
+
+
+
+
+@RunTimeControl
+
+$SimTtl Simulation Title: Martensite C=0.1 wt.%
+$nSteps Number of timesteps: 1000000
+$FTime Output to disk every: 100
+$STime Output to screen every: 100
+$dt Timestep: 5e-4
+$nOMP OpenMP threads: 1
+$tRstrt Restart output every: 1000
+$Restrt Restart switch (Yes or No): No
+$tStart Restart timestep: 0
+$SynchronizeTimeSteps Synchronize timesteps: No
+$PhaseFieldTimeFactor Refinement of phase field step: 1
+$DiffusionTimeFactor Refinement of diffusion step: 1
+$HeatDiffusionFactor Refinement of heat diffusion step: 1
+
+
+
+
+
+@Settings
+
+$Comp_0 Name of Component 0: FE
+$Phase_0 Name of Phase 0: AUSTENITE
+$Phase_1 Name of Phase 1: MARTENSITE
+$dx Grid spacing (dx): 1e-7
+$Nx System size in X direction: 64
+$Ny System size in Y direction: 64
+$Nz System size in Z direction: 64
+$IWidth Interface width: 5.0
+$MoveFrameDirection Move frame direction: No
+$MoveFramePosition Move frame position: 0
+$MoveFramePhase Move frame phase: 0
+
+
+
+
+
+@SymmetryVariants
+
+
+
+
+
+$Nvariants_0 : 0
+
+$Nvariants_1 : 0
+
+
+@Temperature
+
+$ReadfromFile Obtain temperature curve from file: No
+$DataFile Data file containing temperature curve: *.opit
+$T0 Initial System Temperature: 940.0
+$R0X X coordinate of the reference point: 0.0
+$R0Y Y coordinate of the reference point: 0.0
+$R0Z Z coordinate of the reference point: 0.0
+$DT_DRX X component of the temp. gradient: 0.0
+$DT_DRY Y component of the temp. gradient: 0
+$DT_DRZ Z component of the temp. gradient: 0
+$DT_Dt Cooling(-) or heating(+) rate: -100.0
+$LatentHeat Latent heat mode: No
+$LAT_HEAT_0_0 Latent heat: 0.0
+$LAT_HEAT_0_1 Latent heat: 0.0
+$LAT_HEAT_1_1 Latent heat: 0.0
+
+
+
+
+
+@UserDrivingForce
+
+$UDF_Mode_0_1 : FORMULA
+$UDF_LatentHeat_0_1 Latent Heat: 9.03e8
+$UDF_Teq_0_1 Equilibrium Temperature: 990
+