| 6 |
|
* redistribute this software in source and binary code form, provided |
| 7 |
|
* that the following conditions are met: |
| 8 |
|
* |
| 9 |
< |
* 1. Acknowledgement of the program authors must be made in any |
| 10 |
< |
* publication of scientific results based in part on use of the |
| 11 |
< |
* program. An acceptable form of acknowledgement is citation of |
| 12 |
< |
* the article in which the program was described (Matthew |
| 13 |
< |
* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher |
| 14 |
< |
* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented |
| 15 |
< |
* Parallel Simulation Engine for Molecular Dynamics," |
| 16 |
< |
* J. Comput. Chem. 26, pp. 252-271 (2005)) |
| 17 |
< |
* |
| 18 |
< |
* 2. Redistributions of source code must retain the above copyright |
| 9 |
> |
* 1. Redistributions of source code must retain the above copyright |
| 10 |
|
* notice, this list of conditions and the following disclaimer. |
| 11 |
|
* |
| 12 |
< |
* 3. Redistributions in binary form must reproduce the above copyright |
| 12 |
> |
* 2. Redistributions in binary form must reproduce the above copyright |
| 13 |
|
* notice, this list of conditions and the following disclaimer in the |
| 14 |
|
* documentation and/or other materials provided with the |
| 15 |
|
* distribution. |
| 28 |
|
* arising out of the use of or inability to use software, even if the |
| 29 |
|
* University of Notre Dame has been advised of the possibility of |
| 30 |
|
* such damages. |
| 31 |
+ |
* |
| 32 |
+ |
* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your |
| 33 |
+ |
* research, please cite the appropriate papers when you publish your |
| 34 |
+ |
* work. Good starting points are: |
| 35 |
+ |
* |
| 36 |
+ |
* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
| 37 |
+ |
* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |
| 38 |
+ |
* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008). |
| 39 |
+ |
* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
| 40 |
+ |
* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
| 41 |
|
*/ |
| 42 |
|
|
| 43 |
|
#include "selection/SelectionCompiler.hpp" |
| 44 |
|
#include "utils/StringUtils.hpp" |
| 45 |
< |
namespace oopse { |
| 45 |
> |
namespace OpenMD { |
| 46 |
|
|
| 47 |
< |
bool SelectionCompiler::compile(const std::string& filename, const std::string& script) { |
| 47 |
> |
bool SelectionCompiler::compile(const std::string& filename, |
| 48 |
> |
const std::string& script) { |
| 49 |
|
|
| 50 |
|
this->filename = filename; |
| 51 |
|
this->script = script; |
| 119 |
|
// ltoken.push_back(Token(Token::string, str)); |
| 120 |
|
// continue; |
| 121 |
|
//} |
| 122 |
< |
if (lookingAtDecimal((tokCommand & Token::negnums) != 0)) { |
| 122 |
> |
//if (lookingAtDecimal((tokCommand & Token::negnums) != 0)) { |
| 123 |
> |
if (lookingAtDecimal((tokCommand) != 0)) { |
| 124 |
|
float value = lexi_cast<float>(script.substr(ichToken, cchToken)); |
| 125 |
|
ltoken.push_back(Token(Token::decimal, boost::any(value))); |
| 126 |
|
continue; |
| 127 |
|
} |
| 128 |
< |
if (lookingAtInteger((tokCommand & Token::negnums) != 0)) { |
| 128 |
> |
//if (lookingAtInteger((tokCommand & Token::negnums) != 0)) { |
| 129 |
> |
if (lookingAtInteger((tokCommand) != 0)) { |
| 130 |
|
|
| 131 |
|
int val = lexi_cast<int>(script.substr(ichToken, cchToken)); |
| 132 |
|
ltoken.push_back(Token(Token::integer, boost::any(val))); |
| 179 |
|
continue; |
| 180 |
|
} |
| 181 |
|
|
| 182 |
< |
if (ltoken.size() == 0) { |
| 182 |
> |
if (ltoken.empty()) { |
| 183 |
|
return commandExpected(); |
| 184 |
|
} |
| 185 |
|
|
| 443 |
|
|
| 444 |
|
bool SelectionCompiler::compileExpression() { |
| 445 |
|
/** todo */ |
| 446 |
< |
int i = 1; |
| 446 |
> |
unsigned int i = 1; |
| 447 |
|
int tokCommand = atokenCommand[0].tok; |
| 448 |
|
if (tokCommand == Token::define) { |
| 449 |
|
i = 2; |
| 575 |
|
// fall into the code and below and just add the token |
| 576 |
|
case Token::all: |
| 577 |
|
case Token::none: |
| 578 |
+ |
case Token::hull: |
| 579 |
|
return addTokenToPostfix(tokenNext()); |
| 580 |
|
case Token::leftparen: |
| 581 |
|
tokenNext(); |
| 668 |
|
bool SelectionCompiler::isNameValid(const std::string& name) { |
| 669 |
|
int nbracket = 0; |
| 670 |
|
int ndot = 0; |
| 671 |
< |
for (int i =0 ; i < name.size(); ++i) { |
| 671 |
> |
for (unsigned int i = 0 ; i < name.size(); ++i) { |
| 672 |
|
switch(name[i]) { |
| 673 |
|
|
| 674 |
|
case '[' : |
