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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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27
lib/atc/PerAtomQuantityLibrary.cpp
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@ -4,6 +4,17 @@
#include "FE_Engine.h"
#include "LammpsInterface.h"
#include <typeinfo>
#include <sstream>
#include <iostream>
using std::map;
using std::ifstream;
using std::stringstream;
using std::set;
using std::string;
using std::vector;
using ATC_Utility::to_string;
namespace ATC {
@ -96,10 +107,11 @@ namespace ATC {
INT_ARRAY map = map_->quantity();
int * type = ATC::LammpsInterface::instance()->atom_type();
ESET::const_iterator itr;
const Array<int> & quantityToLammps = atc_.atc_to_lammps_map();
for (int i = 0; i < map.size(); i++) {
for (itr=eset_.begin(); itr != eset_.end(); itr++) {
if (map(i,0) == *itr) {
int a = quantityToLammps_(i);
int a = quantityToLammps(i);
if (type[a] == type_) {
list_.push_back(ID_PAIR(i,a));
break;
@ -577,10 +589,11 @@ namespace ATC {
//PerAtomQuantity<double>::reset();
int nlocal = atc_->nlocal();
quantity_.reset(nlocal,typeList_.size()+groupList_.size());
const Array<int> & quantityToLammps = (PerAtomQuantity<double>::atc_).atc_to_lammps_map();
if (typeList_.size()) {
int * type = ATC::LammpsInterface::instance()->atom_type();
for (int i = 0; i < nlocal; i++) {
int a = quantityToLammps_(i);
int a = quantityToLammps(i);
int index = index_[type[a]-1];
if (index > -1) quantity_(i,index) = 1;
}
@ -591,7 +604,7 @@ namespace ATC {
for (unsigned int j = 0; j < groupList_.size(); j++) {
int group = groupList_[j];
for (int i = 0; i < nlocal; i++) {
int a = quantityToLammps_(i);
int a = quantityToLammps(i);
if (mask[a] & group) quantity_(i,index) = 1;
}
index++;
@ -1539,8 +1552,9 @@ namespace ATC {
size_ = 0;
const int * type = lammpsInterface_->atom_type();
const Array<int> & quantityToLammps = atc_.atc_to_lammps_map();
for (int i = 0; i < quantity_.nRows(); ++i) {
int atomIdx = quantityToLammps_(i);
int atomIdx = quantityToLammps(i);
if (type[atomIdx] == type_) {
quantity_(i,0) = size_;
++size_;
@ -1579,8 +1593,9 @@ namespace ATC {
size_ = 0;
const int * mask = lammpsInterface_->atom_mask();
const Array<int> & quantityToLammps = atc_.atc_to_lammps_map();
for (int i = 0; i < quantity_.nRows(); ++i) {
int atomIdx = quantityToLammps_(i);
int atomIdx = quantityToLammps(i);
if (mask[atomIdx] & group_) {
quantity_(i,0) = size_;
++size_;
@ -2117,7 +2132,7 @@ namespace ATC {
PerAtomKernelFunction::PerAtomKernelFunction(ATC_Method * atc,
PerAtomQuantity<double> * atomPositions,
AtomType atomType) :
ProtectedAtomSparseMatrix<double>(atc,(atc->fe_engine())->num_nodes(),(atc->fe_engine())->num_nodes(),atomType),
ProtectedAtomSparseMatrix<double>(atc,(atc->fe_engine())->num_nodes(),atc->accumulant_bandwidth(),atomType),
atomPositions_(atomPositions),
feEngine_(atc->fe_engine())
{