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replace tabs and remove trailing whitespace in lib folder with updated script

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This commit is contained in:
Axel Kohlmeyer
2021-08-22 20:45:24 -04:00
parent 30821b37e5
commit 92b5b159e5
311 changed files with 9176 additions and 9176 deletions
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76
lib/atc/ATC_TransferKernel.cpp
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@ -1,4 +1,4 @@
// ATC headers
// ATC headers
#include "ATC_TransferKernel.h"
#include "ATC_Error.h"
#include "FE_Engine.h"
@ -44,10 +44,10 @@ using ATC_Utility::to_string;
{
bool match = false;
/*! \page man_hardy_kernel fix_modify AtC kernel
/*! \page man_hardy_kernel fix_modify AtC kernel
\section syntax
fix_modify AtC kernel <type> <parameters>
- type (keyword) = step, cell, cubic_bar, cubic_cylinder, cubic_sphere,
- type (keyword) = step, cell, cubic_bar, cubic_cylinder, cubic_sphere,
quartic_bar, quartic_cylinder, quartic_sphere \n
- parameters :\n
step = radius (double) \n
@ -62,7 +62,7 @@ using ATC_Utility::to_string;
<TT> fix_modify AtC kernel cell 1.0 1.0 1.0 </TT> \n
<TT> fix_modify AtC kernel quartic_sphere 10.0 </TT>
\section description
\section restrictions
Must be used with the hardy AtC fix \n
For bar kernel types, half-width oriented along x-direction \n
@ -92,28 +92,28 @@ using ATC_Utility::to_string;
SPAR_MAT & dN(kernelAccumulantMolGrad_.set_quantity());
dN.reset(nLocalMol,nNodes_);
DENS_VEC derivKer(nsd_);
DENS_VEC xI(nsd_),xm(nsd_),xmI(nsd_);
DENS_VEC xI(nsd_),xm(nsd_),xmI(nsd_);
const DENS_MAT & centroidMolMatrix(moleculeCentroid_->quantity());
ATC::LammpsInterface::instance()->stream_msg_once("computing kernel matrix molecule ",true,false);
int heartbeatFreq = (nNodes_ <= 10 ? 1 : (int) nNodes_ / 10);
ATC::LammpsInterface::instance()->stream_msg_once("computing kernel matrix molecule ",true,false);
int heartbeatFreq = (nNodes_ <= 10 ? 1 : (int) nNodes_ / 10);
for (int i = 0; i < nNodes_; i++) {
if (i % heartbeatFreq == 0 ) {
if (i % heartbeatFreq == 0 ) {
ATC::LammpsInterface::instance()->stream_msg_once(".",false,false);
}
}
xI = (feEngine_->fe_mesh())->nodal_coordinates(i);
for (int j = 0; j < nLocalMol; j++) {
for (int k = 0; k < nsd_; k++) {
xm(k) = centroidMolMatrix(j,k);
}
xmI = xm - xI;
xmI = xm - xI;
lammpsInterface_->periodicity_correction(xmI.ptr());
double val = kernelFunction_->value(xmI);
if (val > 0) N.add(j,i,val);
kernelFunction_->derivative(xmI,derivKer);
double val_grad = derivKer(2);
if (val_grad!= 0) dN.add(j,i,val_grad);
}
}
}
}
// reset kernelShpFunctions with the weights of molecules on processors
DENS_VEC fractions(N.nRows());
DENS_VEC fractions_deriv(dN.nRows());
@ -126,10 +126,10 @@ using ATC_Utility::to_string;
dN.compress();
if (lammpsInterface_->rank_zero()) {
ATC::LammpsInterface::instance()->stream_msg_once("done",false,true);
}
}
}
}
}
//-------------------------------------------------------------------
void ATC_TransferKernel::compute_projection(const DENS_MAT & atomData,
DENS_MAT & nodeData)
@ -183,7 +183,7 @@ using ATC_Utility::to_string;
int **firstneigh = lammpsInterface_->neighbor_list_firstneigh();
double ** xatom = lammpsInterface_->xatom();
double lam1,lam2;
double bond_value;
double bond_value;
// process differently for mesh vs translation-invariant kernels
ATC::LammpsInterface::instance()->stream_msg_once("computing potential stress: ",true,false);
int heartbeatFreq = (nNodes_ <= 10 ? 1 : (int) nNodes_ / 10);
@ -202,7 +202,7 @@ using ATC_Utility::to_string;
int inode = i;
for (int j = 0; j < nLocal_; j++) {
// second (neighbor) atom location
int lammps_j = internalToAtom_(j);
int lammps_j = internalToAtom_(j);
xa.copy(xPointer_[lammps_j],3);
// difference vector
xaI = xa - xI;
@ -217,8 +217,8 @@ using ATC_Utility::to_string;
kernelFunction_->bond_intercepts(xaI,xbI,lam1,lam2);
// compute virial
if (lam1 < lam2) {
bond_value
= kernel_inv_vol*(kernelFunction_->bond(xaI,xbI,lam1,lam2));
bond_value
= kernel_inv_vol*(kernelFunction_->bond(xaI,xbI,lam1,lam2));
double delx = xatom[lammps_j][0] - xatom[lammps_k][0];
double dely = xatom[lammps_j][1] - xatom[lammps_k][1];
double delz = xatom[lammps_j][2] - xatom[lammps_k][2];
@ -227,9 +227,9 @@ using ATC_Utility::to_string;
lammpsInterface_->pair_force(lammps_j,lammps_k,rsq,fforce);
fforce *= 0.5; // dbl count
if (atomToElementMapType_ == LAGRANGIAN) {
double delX = xref_[lammps_j][0] - xref_[lammps_k][0];
double delY = xref_[lammps_j][1] - xref_[lammps_k][1];
double delZ = xref_[lammps_j][2] - xref_[lammps_k][2];
double delX = xref_[lammps_j][0] - xref_[lammps_k][0];
double delY = xref_[lammps_j][1] - xref_[lammps_k][1];
double delZ = xref_[lammps_j][2] - xref_[lammps_k][2];
stress(inode,0) +=-delx*fforce*delX*bond_value;
stress(inode,1) +=-delx*fforce*delY*bond_value;
stress(inode,2) +=-delx*fforce*delZ*bond_value;
@ -266,9 +266,9 @@ using ATC_Utility::to_string;
int **firstneigh = lammpsInterface_->neighbor_list_firstneigh();
double ** xatom = lammpsInterface_->xatom();
double ** vatom = lammpsInterface_->vatom();
double lam1,lam2;
double bond_value;
double bond_value;
// process differently for mesh vs translation-invariant kernels
// "normal" kernel functions
DENS_VEC xa(nsd_),xI(nsd_),xaI(nsd_),xb(nsd_),xbI(nsd_),xba(nsd_);
@ -281,7 +281,7 @@ using ATC_Utility::to_string;
continue;
}
for (int j = 0; j < nLocal_; j++) {
int lammps_j = internalToAtom_(j);
int lammps_j = internalToAtom_(j);
xa.copy(xPointer_[lammps_j],3);
// difference vector
xaI = xa - xI;
@ -296,8 +296,8 @@ using ATC_Utility::to_string;
kernelFunction_->bond_intercepts(xaI,xbI,lam1,lam2);
// compute virial
if (lam1 < lam2) {
bond_value
= kernel_inv_vol*(kernelFunction_->bond(xaI,xbI,lam1,lam2));
bond_value
= kernel_inv_vol*(kernelFunction_->bond(xaI,xbI,lam1,lam2));
double delx = xatom[lammps_j][0] - xatom[lammps_k][0];
double dely = xatom[lammps_j][1] - xatom[lammps_k][1];
double delz = xatom[lammps_j][2] - xatom[lammps_k][2];
@ -308,9 +308,9 @@ using ATC_Utility::to_string;
double * v = vatom[lammps_j];
fforce *= (delx*v[0] + dely*v[1] + delz*v[2]);
if (atomToElementMapType_ == LAGRANGIAN) {
double delX = xref_[lammps_j][0] - xref_[lammps_k][0];
double delY = xref_[lammps_j][1] - xref_[lammps_k][1];
double delZ = xref_[lammps_j][2] - xref_[lammps_k][2];
double delX = xref_[lammps_j][0] - xref_[lammps_k][0];
double delY = xref_[lammps_j][1] - xref_[lammps_k][1];
double delZ = xref_[lammps_j][2] - xref_[lammps_k][2];
flux(inode,0) +=fforce*delX*bond_value;
flux(inode,1) +=fforce*delY*bond_value;
flux(inode,2) +=fforce*delZ*bond_value;
@ -327,7 +327,7 @@ using ATC_Utility::to_string;
}
//-------------------------------------------------------------------
// calculation of the dislocation density tensor
// calculation of the dislocation density tensor
void ATC_TransferKernel::compute_dislocation_density(DENS_MAT & A)
{
A.reset(nNodes_,9);
@ -348,7 +348,7 @@ using ATC_Utility::to_string;
lammpsInterface_->int_allsum(&localNumberLines,&totalNumberLines,1);
if (totalNumberLines == 0) {
ATC::LammpsInterface::instance()->print_msg_once("no dislocation lines found");
return;
return;
}
// for output
@ -366,7 +366,7 @@ using ATC_Utility::to_string;
DENS_MAT local_A(nNodes_,9);
local_A.zero();
local_A.zero();
DENS_VEC xa(nsd_),xI(nsd_),xaI(nsd_),xb(nsd_),xbI(nsd_),xba(nsd_);
double kernel_inv_vol = kernelFunction_->inv_vol();
int iPt = 0, iSeg= 0;
@ -393,7 +393,7 @@ using ATC_Utility::to_string;
xa(k) = x1[k];
xb(k) = x2[k];
xba(k) = delta[k];
}
}
for (int I = 0; I < nNodes_; I++) {
xI = (feEngine_->fe_mesh())->nodal_coordinates(I);
if (!kernelFunction_->node_contributes(xI)) {
@ -405,7 +405,7 @@ using ATC_Utility::to_string;
double lam1=0,lam2=0;
kernelFunction_->bond_intercepts(xaI,xbI,lam1,lam2);
if (lam1 < lam2) {
double bond_value
double bond_value
= kernel_inv_vol*(kernelFunction_->bond(xaI,xbI,lam1,lam2));
local_A(I,0) += xba(0)*burgers[0]*bond_value;
local_A(I,1) += xba(0)*burgers[1]*bond_value;
@ -449,7 +449,7 @@ using ATC_Utility::to_string;
lammpsInterface_->int_allsum(&nSeg,&totalNumberSegments,1);
// output
double volume = lammpsInterface_->domain_volume();
double volume = lammpsInterface_->domain_volume();
stringstream ss;
ss << "total dislocation line length = " << totalDislocationDensity;
ss << " lines = " << totalNumberLines << " segments = " << totalNumberSegments;
@ -474,10 +474,10 @@ using ATC_Utility::to_string;
segOutput.write_geometry(&segCoor,&segConn);
OUTPUT_LIST segOut;
segOut["burgers_vector"] = &segBurg;
segOutput.write_data(0,&segOut);
segOutput.write_data(0,&segOut);
}
#else
throw ATC_Error("unimplemented function compute_dislocation_density (DXA support not included");
throw ATC_Error("unimplemented function compute_dislocation_density (DXA support not included");
#endif
}