| 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, 24107 (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 |
|
|
| 55 |
|
#include <bitset> |
| 56 |
|
#include <fstream> |
| 57 |
|
#include <iostream> |
| 58 |
+ |
#include <string> |
| 59 |
|
#include <string.h> |
| 60 |
|
|
| 61 |
|
#include "brains/Stats.hpp" |
| 62 |
+ |
#include "utils/StringTokenizer.hpp" |
| 63 |
+ |
#include "utils/CaseConversion.hpp" |
| 64 |
+ |
#include "utils/simError.h" |
| 65 |
|
|
| 66 |
< |
namespace oopse { |
| 66 |
> |
namespace OpenMD { |
| 67 |
|
|
| 68 |
|
typedef std::bitset<Stats::ENDINDEX-Stats::BEGININDEX> StatsBitSet; |
| 69 |
|
|
| 70 |
+ |
StatsBitSet parseStatFileFormat(const std::string& format); |
| 71 |
+ |
|
| 72 |
|
/** |
| 66 |
– |
* DefaultStatsBitSet includes |
| 67 |
– |
* StatsIndex::TIME |
| 68 |
– |
* StatsIndex::TOTAL_ENERGY |
| 69 |
– |
* StatsIndex::POTENTIAL_ENERGY |
| 70 |
– |
* StatsIndex::KINETIC_ENERGY |
| 71 |
– |
* StatsIndex::TEMPERATURE |
| 72 |
– |
* StatsIndex::PRESSURE |
| 73 |
– |
* StatsIndex::CONSERVED_QUANTITY |
| 74 |
– |
*/ |
| 75 |
– |
const StatsBitSet DefaultStatsBitSet(255ul); |
| 76 |
– |
|
| 77 |
– |
|
| 78 |
– |
/** |
| 73 |
|
* @class StatWriter StatWriter.hpp "io/StatWriter.hpp" |
| 74 |
|
* @brief A configurable Statistics Writer |
| 75 |
|
*/ |
| 76 |
|
class StatWriter { |
| 77 |
|
public: |
| 78 |
< |
StatWriter(const std::string& filename, const StatsBitSet& mask = DefaultStatsBitSet); |
| 78 |
> |
StatWriter(const std::string& filename, const StatsBitSet& mask); |
| 79 |
|
~StatWriter(); |
| 80 |
|
|
| 81 |
|
void writeStat(const Stats& s); |
