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Clang format (#55)

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Run clang-format on modules of code
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Thomas Ramstad authored and GitHub committed 2021-11-08 22:58:37 +01:00
1 parent f29ae0b0bc
commit 23189f5577
104 files changed
+56746 -49196
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analysis/FreeEnergy.cpp
+122 -112
View File
@@ -1,55 +1,60 @@
#include "analysis/FreeEnergy.h"
FreeEnergyAnalyzer::FreeEnergyAnalyzer(std::shared_ptr <Domain> dm):
Dm(dm)
{
Nx=dm->Nx; Ny=dm->Ny; Nz=dm->Nz;
Volume=(Nx-2)*(Ny-2)*(Nz-2)*Dm->nprocx()*Dm->nprocy()*Dm->nprocz()*1.0;
ChemicalPotential.resize(Nx,Ny,Nz); ChemicalPotential.fill(0);
Phi.resize(Nx,Ny,Nz); Phi.fill(0);
Pressure.resize(Nx,Ny,Nz); Pressure.fill(0);
Rho.resize(Nx,Ny,Nz); Rho.fill(0);
Vel_x.resize(Nx,Ny,Nz); Vel_x.fill(0); // Gradient of the phase indicator field
Vel_y.resize(Nx,Ny,Nz); Vel_y.fill(0);
Vel_z.resize(Nx,Ny,Nz); Vel_z.fill(0);
SDs.resize(Nx,Ny,Nz); SDs.fill(0);
if (Dm->rank()==0){
bool WriteHeader=false;
TIMELOG = fopen("free.csv","r");
if (TIMELOG != NULL)
fclose(TIMELOG);
else
WriteHeader=true;
FreeEnergyAnalyzer::FreeEnergyAnalyzer(std::shared_ptr<Domain> dm) : Dm(dm) {
TIMELOG = fopen("free.csv","a+");
if (WriteHeader)
{
// If timelog is empty, write a short header to list the averages
//fprintf(TIMELOG,"--------------------------------------------------------------------------------------\n");
fprintf(TIMELOG,"timestep\n");
}
}
Nx = dm->Nx;
Ny = dm->Ny;
Nz = dm->Nz;
Volume = (Nx - 2) * (Ny - 2) * (Nz - 2) * Dm->nprocx() * Dm->nprocy() *
Dm->nprocz() * 1.0;
ChemicalPotential.resize(Nx, Ny, Nz);
ChemicalPotential.fill(0);
Phi.resize(Nx, Ny, Nz);
Phi.fill(0);
Pressure.resize(Nx, Ny, Nz);
Pressure.fill(0);
Rho.resize(Nx, Ny, Nz);
Rho.fill(0);
Vel_x.resize(Nx, Ny, Nz);
Vel_x.fill(0); // Gradient of the phase indicator field
Vel_y.resize(Nx, Ny, Nz);
Vel_y.fill(0);
Vel_z.resize(Nx, Ny, Nz);
Vel_z.fill(0);
SDs.resize(Nx, Ny, Nz);
SDs.fill(0);
if (Dm->rank() == 0) {
bool WriteHeader = false;
TIMELOG = fopen("free.csv", "r");
if (TIMELOG != NULL)
fclose(TIMELOG);
else
WriteHeader = true;
TIMELOG = fopen("free.csv", "a+");
if (WriteHeader) {
// If timelog is empty, write a short header to list the averages
//fprintf(TIMELOG,"--------------------------------------------------------------------------------------\n");
fprintf(TIMELOG, "timestep\n");
}
}
}
FreeEnergyAnalyzer::~FreeEnergyAnalyzer(){
if (Dm->rank()==0){
fclose(TIMELOG);
}
FreeEnergyAnalyzer::~FreeEnergyAnalyzer() {
if (Dm->rank() == 0) {
fclose(TIMELOG);
}
}
void FreeEnergyAnalyzer::SetParams(){
}
void FreeEnergyAnalyzer::SetParams() {}
void FreeEnergyAnalyzer::Basic(ScaLBL_FreeLeeModel &LeeModel, int timestep){
void FreeEnergyAnalyzer::Basic(ScaLBL_FreeLeeModel &LeeModel, int timestep) {
if (Dm->rank()==0){
fprintf(TIMELOG,"%i ",timestep);
/*for (int ion=0; ion<Ion.number_ion_species; ion++){
if (Dm->rank() == 0) {
fprintf(TIMELOG, "%i ", timestep);
/*for (int ion=0; ion<Ion.number_ion_species; ion++){
fprintf(TIMELOG,"%.8g ",rho_avg_global[ion]);
fprintf(TIMELOG,"%.8g ",rho_mu_avg_global[ion]);
fprintf(TIMELOG,"%.8g ",rho_psi_avg_global[ion]);
@@ -57,10 +62,10 @@ void FreeEnergyAnalyzer::Basic(ScaLBL_FreeLeeModel &LeeModel, int timestep){
fprintf(TIMELOG,"%.8g ",rho_psi_fluctuation_global[ion]);
}
*/
fprintf(TIMELOG,"\n");
fflush(TIMELOG);
}
/* else{
fprintf(TIMELOG, "\n");
fflush(TIMELOG);
}
/* else{
fprintf(TIMELOG,"%i ",timestep);
for (int ion=0; ion<Ion.number_ion_species; ion++){
fprintf(TIMELOG,"%.8g ",rho_avg_local[ion]);
@@ -73,106 +78,111 @@ void FreeEnergyAnalyzer::Basic(ScaLBL_FreeLeeModel &LeeModel, int timestep){
} */
}
void FreeEnergyAnalyzer::WriteVis( ScaLBL_FreeLeeModel &LeeModel, std::shared_ptr<Database> input_db, int timestep){
auto vis_db = input_db->getDatabase( "Visualization" );
std::vector<IO::MeshDataStruct> visData;
fillHalo<double> fillData(Dm->Comm,Dm->rank_info,{Dm->Nx-2,Dm->Ny-2,Dm->Nz-2},{1,1,1},0,1);
void FreeEnergyAnalyzer::WriteVis(ScaLBL_FreeLeeModel &LeeModel,
std::shared_ptr<Database> input_db,
int timestep) {
IO::initialize("","silo","false");
// Create the MeshDataStruct
auto vis_db = input_db->getDatabase("Visualization");
std::vector<IO::MeshDataStruct> visData;
fillHalo<double> fillData(Dm->Comm, Dm->rank_info,
{Dm->Nx - 2, Dm->Ny - 2, Dm->Nz - 2}, {1, 1, 1},
0, 1);
IO::initialize("", "silo", "false");
// Create the MeshDataStruct
visData.resize(1);
visData[0].meshName = "domain";
visData[0].mesh = std::make_shared<IO::DomainMesh>( Dm->rank_info,Dm->Nx-2,Dm->Ny-2,Dm->Nz-2,Dm->Lx,Dm->Ly,Dm->Lz );
visData[0].mesh =
std::make_shared<IO::DomainMesh>(Dm->rank_info, Dm->Nx - 2, Dm->Ny - 2,
Dm->Nz - 2, Dm->Lx, Dm->Ly, Dm->Lz);
auto VisPhase = std::make_shared<IO::Variable>();
auto VisPressure = std::make_shared<IO::Variable>();
auto VisChemicalPotential = std::make_shared<IO::Variable>();
auto VxVar = std::make_shared<IO::Variable>();
auto VyVar = std::make_shared<IO::Variable>();
auto VzVar = std::make_shared<IO::Variable>();
if (vis_db->getWithDefault<bool>( "save_phase_field", true )){
VisPhase->name = "Phase";
VisPhase->type = IO::VariableType::VolumeVariable;
VisPhase->dim = 1;
VisPhase->data.resize(Dm->Nx-2,Dm->Ny-2,Dm->Nz-2);
if (vis_db->getWithDefault<bool>("save_phase_field", true)) {
VisPhase->name = "Phase";
VisPhase->type = IO::VariableType::VolumeVariable;
VisPhase->dim = 1;
VisPhase->data.resize(Dm->Nx - 2, Dm->Ny - 2, Dm->Nz - 2);
visData[0].vars.push_back(VisPhase);
}
if (vis_db->getWithDefault<bool>( "save_potential", true )){
VisPressure->name = "Pressure";
VisPressure->type = IO::VariableType::VolumeVariable;
VisPressure->dim = 1;
VisPressure->data.resize(Dm->Nx-2,Dm->Ny-2,Dm->Nz-2);
}
if (vis_db->getWithDefault<bool>("save_potential", true)) {
VisPressure->name = "Pressure";
VisPressure->type = IO::VariableType::VolumeVariable;
VisPressure->dim = 1;
VisPressure->data.resize(Dm->Nx - 2, Dm->Ny - 2, Dm->Nz - 2);
visData[0].vars.push_back(VisPressure);
VisChemicalPotential->name = "ChemicalPotential";
VisChemicalPotential->type = IO::VariableType::VolumeVariable;
VisChemicalPotential->dim = 1;
VisChemicalPotential->data.resize(Dm->Nx-2,Dm->Ny-2,Dm->Nz-2);
VisChemicalPotential->name = "ChemicalPotential";
VisChemicalPotential->type = IO::VariableType::VolumeVariable;
VisChemicalPotential->dim = 1;
VisChemicalPotential->data.resize(Dm->Nx - 2, Dm->Ny - 2, Dm->Nz - 2);
visData[0].vars.push_back(VisChemicalPotential);
}
if (vis_db->getWithDefault<bool>( "save_velocity", false )){
if (vis_db->getWithDefault<bool>("save_velocity", false)) {
VxVar->name = "Velocity_x";
VxVar->type = IO::VariableType::VolumeVariable;
VxVar->dim = 1;
VxVar->data.resize(Dm->Nx-2,Dm->Ny-2,Dm->Nz-2);
VxVar->data.resize(Dm->Nx - 2, Dm->Ny - 2, Dm->Nz - 2);
visData[0].vars.push_back(VxVar);
VyVar->name = "Velocity_y";
VyVar->type = IO::VariableType::VolumeVariable;
VyVar->dim = 1;
VyVar->data.resize(Dm->Nx-2,Dm->Ny-2,Dm->Nz-2);
VyVar->data.resize(Dm->Nx - 2, Dm->Ny - 2, Dm->Nz - 2);
visData[0].vars.push_back(VyVar);
VzVar->name = "Velocity_z";
VzVar->type = IO::VariableType::VolumeVariable;
VzVar->dim = 1;
VzVar->data.resize(Dm->Nx-2,Dm->Ny-2,Dm->Nz-2);
VzVar->data.resize(Dm->Nx - 2, Dm->Ny - 2, Dm->Nz - 2);
visData[0].vars.push_back(VzVar);
}
if (vis_db->getWithDefault<bool>( "save_phase", true )){
ASSERT(visData[0].vars[0]->name=="Phase");
LeeModel.getPhase(Phi);
Array<double>& PhaseData = visData[0].vars[0]->data;
fillData.copy(Phi,PhaseData);
if (vis_db->getWithDefault<bool>("save_phase", true)) {
ASSERT(visData[0].vars[0]->name == "Phase");
LeeModel.getPhase(Phi);
Array<double> &PhaseData = visData[0].vars[0]->data;
fillData.copy(Phi, PhaseData);
}
if (vis_db->getWithDefault<bool>( "save_potential", true )){
ASSERT(visData[0].vars[1]->name=="Pressure");
LeeModel.getPotential(Pressure, ChemicalPotential);
Array<double>& PressureData = visData[0].vars[1]->data;
fillData.copy(Pressure,PressureData);
ASSERT(visData[0].vars[2]->name=="ChemicalPotential");
Array<double>& ChemicalPotentialData = visData[0].vars[2]->data;
fillData.copy(ChemicalPotential,ChemicalPotentialData);
}
if (vis_db->getWithDefault<bool>( "save_velocity", false )){
ASSERT(visData[0].vars[3]->name=="Velocity_x");
ASSERT(visData[0].vars[4]->name=="Velocity_y");
ASSERT(visData[0].vars[5]->name=="Velocity_z");
LeeModel.getVelocity(Vel_x,Vel_y,Vel_z);
Array<double>& VelxData = visData[0].vars[3]->data;
Array<double>& VelyData = visData[0].vars[4]->data;
Array<double>& VelzData = visData[0].vars[5]->data;
fillData.copy(Vel_x,VelxData);
fillData.copy(Vel_y,VelyData);
fillData.copy(Vel_z,VelzData);
}
if (vis_db->getWithDefault<bool>( "write_silo", true ))
IO::writeData( timestep, visData, Dm->Comm );
if (vis_db->getWithDefault<bool>("save_potential", true)) {
ASSERT(visData[0].vars[1]->name == "Pressure");
LeeModel.getPotential(Pressure, ChemicalPotential);
Array<double> &PressureData = visData[0].vars[1]->data;
fillData.copy(Pressure, PressureData);
/* if (vis_db->getWithDefault<bool>( "save_8bit_raw", true )){
ASSERT(visData[0].vars[2]->name == "ChemicalPotential");
Array<double> &ChemicalPotentialData = visData[0].vars[2]->data;
fillData.copy(ChemicalPotential, ChemicalPotentialData);
}
if (vis_db->getWithDefault<bool>("save_velocity", false)) {
ASSERT(visData[0].vars[3]->name == "Velocity_x");
ASSERT(visData[0].vars[4]->name == "Velocity_y");
ASSERT(visData[0].vars[5]->name == "Velocity_z");
LeeModel.getVelocity(Vel_x, Vel_y, Vel_z);
Array<double> &VelxData = visData[0].vars[3]->data;
Array<double> &VelyData = visData[0].vars[4]->data;
Array<double> &VelzData = visData[0].vars[5]->data;
fillData.copy(Vel_x, VelxData);
fillData.copy(Vel_y, VelyData);
fillData.copy(Vel_z, VelzData);
}
if (vis_db->getWithDefault<bool>("write_silo", true))
IO::writeData(timestep, visData, Dm->Comm);
/* if (vis_db->getWithDefault<bool>( "save_8bit_raw", true )){
char CurrentIDFilename[40];
sprintf(CurrentIDFilename,"id_t%d.raw",timestep);
Averages.AggregateLabels(CurrentIDFilename);
}
*/
*/
}