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ATC version 2.0, date: Aug21

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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10638 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
rjones
2013-08-21 23:06:07 +00:00
parent 0f69054d68
commit d77ab2f96a
161 changed files with 3811 additions and 2548 deletions
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58
lib/atc/PerAtomQuantity-inl.h
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@ -1,6 +1,8 @@
#ifndef PER_ATOM_QUANTITY_INL_H
#define PER_ATOM_QUANTITY_INL_H
#include <string>
namespace ATC {
//--------------------------------------------------------
@ -66,17 +68,18 @@ namespace ATC {
// map quantities
else {
int atomIndex;
const Array<int> & quantityToLammps = atc_.atc_to_lammps_map();
if (nCols_==1) { // scalar
T * lammpsQuantity = this->lammps_scalar();
for (int i = 0; i < myQuantity.nRows(); i++) {
atomIndex = quantityToLammps_(i);
atomIndex = quantityToLammps(i);
lammpsQuantity[atomIndex] = myQuantity(i,0);
}
}
else{ // vector
T ** lammpsQuantity = this->lammps_vector();
for (int i = 0; i < myQuantity.nRows(); i++) {
atomIndex = quantityToLammps_(i);
atomIndex = quantityToLammps(i);
for (int j = 0; j < nCols_; j++) {
lammpsQuantity[atomIndex][j] = myQuantity(i,j);
}
@ -114,19 +117,20 @@ namespace ATC {
}
// map quantities
else {
const Array<int> & quantityToLammps = atc_.atc_to_lammps_map();
int atomIndex;
if (nCols_==1) { // scalar
const T * lammpsQuantity = this->lammps_scalar();
for (int i = 0; i < myQuantity.nRows(); i++) {
atomIndex = quantityToLammps_(i);
atomIndex = quantityToLammps(i);
myQuantity(i,0) = lammpsQuantity[atomIndex];
}
}
else {
const T * const * lammpsQuantity = this->lammps_vector();
for (int i = 0; i < myQuantity.nRows(); i++) {
atomIndex = quantityToLammps_(i);
atomIndex = quantityToLammps(i);
for (int j = 0; j < nCols_; j++) {
myQuantity(i,j) = lammpsQuantity[atomIndex][j];
}
@ -201,7 +205,7 @@ namespace ATC {
// allocate local atom-based arrays
//-----------------------------------------------------------------
template <typename T>
void PerAtomQuantity<T>::grow_lammps_array(int nmax, const string & tag)
void PerAtomQuantity<T>::grow_lammps_array(int nmax, const std::string & tag)
{
if (nCols_ == 1)
@ -341,12 +345,13 @@ namespace ATC {
// map quantities
else {
int atomIndex;
const Array<int> & quantityToLammps = (PerAtomQuantity<T>::atc_).atc_to_lammps_map();
if (nCols==1) { // scalar
T * lammpsQuantity = ProtectedAtomQuantity<T>::lammps_scalar();
for (int i = 0; i < atomMap.nRows(); i++) {
int idx = atomMap(i,0);
if (idx > -1) {
atomIndex = ProtectedAtomQuantity<T>::quantityToLammps_(i);
atomIndex = quantityToLammps(i);
lammpsQuantity[atomIndex] = myQuantity(idx,0);
}
}
@ -356,7 +361,7 @@ namespace ATC {
for (int i = 0; i < atomMap.nRows(); i++) {
int idx = atomMap(i,0);
if (idx > -1) {
atomIndex = ProtectedAtomQuantity<T>::quantityToLammps_(i);
atomIndex = quantityToLammps(i);
for (int j = 0; j < nCols; j++) {
lammpsQuantity[atomIndex][j] = myQuantity(idx,j);
}
@ -403,13 +408,13 @@ namespace ATC {
// map quantities
else {
int atomIndex;
const Array<int> & quantityToLammps = (PerAtomQuantity<T>::atc_).atc_to_lammps_map();
if (nCols==1) { // scalar
const T * lammpsQuantity = ProtectedAtomQuantity<T>::lammps_scalar();
for (int i = 0; i < atomMap.nRows(); i++) {
int idx = atomMap(i,0);
if (idx > -1) {
atomIndex = ProtectedAtomQuantity<T>::quantityToLammps_(i);
atomIndex = quantityToLammps(i);
myQuantity(idx,0) = lammpsQuantity[atomIndex];
}
}
@ -419,7 +424,7 @@ namespace ATC {
for (int i = 0; i < atomMap.nRows(); i++) {
int idx = atomMap(i,0);
if (idx > -1) {
atomIndex = ProtectedAtomQuantity<T>::quantityToLammps_(i);
atomIndex = quantityToLammps(i);
for (int j = 0; j < nCols; j++) {
myQuantity(idx,j) = lammpsQuantity[atomIndex][j];
}
@ -481,9 +486,10 @@ namespace ATC {
// map quantities
else {
int atomIndex;
const Array<int> & quantityToLammps = atc_.atc_to_lammps_map();
T * lammpsQuantity = this->lammps_scalar();
for (int i = 0; i < myQuantity.nRows(); i++) {
atomIndex = quantityToLammps_(i);
atomIndex = quantityToLammps(i);
lammpsQuantity[atomIndex] = myQuantity(i,i);
}
}
@ -509,9 +515,10 @@ namespace ATC {
// map quantities
else {
int atomIndex;
const Array<int> & quantityToLammps = atc_.atc_to_lammps_map();
const T * lammpsQuantity = this->lammps_scalar();
for (int i = 0; i < myQuantity.nRows(); i++) {
atomIndex = quantityToLammps_(i);
atomIndex = quantityToLammps(i);
myQuantity(i,i) = lammpsQuantity[atomIndex];
}
}
@ -567,7 +574,7 @@ namespace ATC {
// allocate local atom-based arrays
//-----------------------------------------------------------------
template <typename T>
void PerAtomDiagonalMatrix<T>::grow_lammps_array(int nmax, const string & tag)
void PerAtomDiagonalMatrix<T>::grow_lammps_array(int nmax, const std::string & tag)
{
this->lammpsScalar_ = lammpsInterface_->grow_array(this->lammpsScalar_,nmax,tag.c_str());
}
@ -647,16 +654,18 @@ namespace ATC {
// map quantities
else {
int atomIndex;
const Array<int> & quantityToLammps = atc_.atc_to_lammps_map();
T ** lammpsQuantity = this->lammps_vector();
int ** lammpsColIndices = this->lammps_column_indices();
for (int i = 0; i < myQuantity.nRows(); i++) {
myQuantity.row(i,_values_,_colIndices_);
atomIndex = quantityToLammps_(i);
atomIndex = quantityToLammps(i);
for (int j = 0; j < _values_.size(); j++) {
lammpsQuantity[atomIndex][j] = _values_(j);
lammpsColIndices[atomIndex][j] = _colIndices_(j);
}
for (int j = _values_.size(); j < maxEntriesPerRow_; j++) {
lammpsQuantity[atomIndex][j] = 0;
lammpsColIndices[atomIndex][j] = -1;
}
}
@ -689,10 +698,11 @@ namespace ATC {
// map quantities
else {
int atomIndex;
const Array<int> & quantityToLammps = atc_.atc_to_lammps_map();
const T * const * lammpsQuantity = this->lammps_vector();
const int * const * lammpsColIndices = this->lammps_column_indices();
for (int i = 0; i < myQuantity.nRows(); i++) {
atomIndex = quantityToLammps_(i);
atomIndex = quantityToLammps(i);
for (int j = 0; j < maxEntriesPerRow_; j++) {
if (lammpsColIndices[atomIndex][j] < 0) {
break;
@ -713,12 +723,12 @@ namespace ATC {
int PerAtomSparseMatrix<T>::pack_exchange(int i, double *buffer)
{
int idx = 0;
T ** lammpsVector = this->lammps_vector();
for (int j = 0; j < maxEntriesPerRow_; j++) {
T ** lammpsVector = this->lammps_vector();
buffer[idx++] = static_cast<double>(lammpsVector[i][j]);
}
int ** lammpsColIndices = this->lammps_column_indices();
for (int j = 0; j < maxEntriesPerRow_; j++) {
int ** lammpsColIndices = this->lammps_column_indices();
buffer[idx++] = static_cast<double>(lammpsColIndices[i][j]);
}
return 2*maxEntriesPerRow_;
@ -731,12 +741,12 @@ namespace ATC {
int PerAtomSparseMatrix<T>::unpack_exchange(int i, double *buffer)
{
int idx = 0;
T ** lammpsVector = this->lammps_vector();
for (int j = 0; j < maxEntriesPerRow_; j++) {
T ** lammpsVector = this->lammps_vector();
lammpsVector[i][j] = static_cast<T>(buffer[idx++]);
}
int ** lammpsColIndices = this->lammps_column_indices();
for (int j = 0; j < maxEntriesPerRow_; j++) {
int ** lammpsColIndices = this->lammps_column_indices();
lammpsColIndices[i][j] = static_cast<int>(buffer[idx++]);
}
return 2*maxEntriesPerRow_;
@ -749,7 +759,7 @@ namespace ATC {
int PerAtomSparseMatrix<T>::pack_comm(int index, double *buf,
int pbc_flag, int *pbc)
{
return maxEntriesPerRow_;
return 0;
}
//-----------------------------------------------------------------
@ -758,18 +768,18 @@ namespace ATC {
template <typename T>
int PerAtomSparseMatrix<T>::unpack_comm(int index, double *buf)
{
return maxEntriesPerRow_;
return 0;
}
//-----------------------------------------------------------------
// allocate local atom-based arrays
//-----------------------------------------------------------------
template <typename T>
void PerAtomSparseMatrix<T>::grow_lammps_array(int nmax, const string & tag)
void PerAtomSparseMatrix<T>::grow_lammps_array(int nmax, const std::string & tag)
{
this->lammpsVector_ = lammpsInterface_->grow_array(this->lammpsVector_,nmax,maxEntriesPerRow_,tag.c_str());
string myString(tag+string("Columns"));
std::string myString(tag+std::string("Columns"));
this->lammpsColIndices_ = lammpsInterface_->grow_array(this->lammpsColIndices_,nmax,maxEntriesPerRow_,myString.c_str());
}