1 |
/* |
2 |
* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. |
3 |
* |
4 |
* The University of Notre Dame grants you ("Licensee") a |
5 |
* non-exclusive, royalty free, license to use, modify and |
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 |
19 |
* notice, this list of conditions and the following disclaimer. |
20 |
* |
21 |
* 3. Redistributions in binary form must reproduce the above copyright |
22 |
* notice, this list of conditions and the following disclaimer in the |
23 |
* documentation and/or other materials provided with the |
24 |
* distribution. |
25 |
* |
26 |
* This software is provided "AS IS," without a warranty of any |
27 |
* kind. All express or implied conditions, representations and |
28 |
* warranties, including any implied warranty of merchantability, |
29 |
* fitness for a particular purpose or non-infringement, are hereby |
30 |
* excluded. The University of Notre Dame and its licensors shall not |
31 |
* be liable for any damages suffered by licensee as a result of |
32 |
* using, modifying or distributing the software or its |
33 |
* derivatives. In no event will the University of Notre Dame or its |
34 |
* licensors be liable for any lost revenue, profit or data, or for |
35 |
* direct, indirect, special, consequential, incidental or punitive |
36 |
* damages, however caused and regardless of the theory of liability, |
37 |
* arising out of the use of or inability to use software, even if the |
38 |
* University of Notre Dame has been advised of the possibility of |
39 |
* such damages. |
40 |
*/ |
41 |
|
42 |
#include "io/DirectionalAtomTypesSectionParser.hpp" |
43 |
#include "UseTheForce/ForceField.hpp" |
44 |
#include "types/DirectionalAtomType.hpp" |
45 |
|
46 |
namespace oopse { |
47 |
|
48 |
DirectionalAtomTypesSectionParser::DirectionalAtomTypesSectionParser() { |
49 |
setSectionName("DirectionalAtomTypes"); |
50 |
} |
51 |
|
52 |
void DirectionalAtomTypesSectionParser::parseLine(ForceField& ff,const std::string& line, int lineNo){ |
53 |
StringTokenizer tokenizer(line); |
54 |
int nTokens = tokenizer.countTokens(); |
55 |
|
56 |
//in AtomTypeSection, a line at least contains 2 tokens |
57 |
//atomTypeName and mass |
58 |
if (nTokens < 4) { |
59 |
std::cerr << "DirectionalAtomTypesSectionParser:: Not enought Tokens" << std::endl; |
60 |
} else { |
61 |
|
62 |
std::string atomTypeName = tokenizer.nextToken(); |
63 |
AtomType* atomType = ff.getAtomType(atomTypeName); |
64 |
DirectionalAtomType* dAtomType; |
65 |
if (atomType == NULL) { |
66 |
dAtomType = new DirectionalAtomType(); |
67 |
int ident = ff.getNAtomType() + 1; |
68 |
dAtomType->setIdent(ident); |
69 |
dAtomType->setName(atomTypeName); |
70 |
ff.addAtomType(atomTypeName, dAtomType); |
71 |
} else { |
72 |
dAtomType = dynamic_cast<DirectionalAtomType*>(atomType); |
73 |
if (dAtomType == NULL) { |
74 |
std::cerr << "DirectionalAtomTypesSectionParser:: Can not cast to DirectionalAtomType" << std::endl; |
75 |
} |
76 |
} |
77 |
|
78 |
double Ixx = tokenizer.nextTokenAsDouble(); |
79 |
double Iyy = tokenizer.nextTokenAsDouble(); |
80 |
double Izz = tokenizer.nextTokenAsDouble(); |
81 |
Mat3x3d inertialMat; |
82 |
inertialMat(0, 0) = Ixx; |
83 |
inertialMat(1, 1) = Iyy; |
84 |
inertialMat(2, 2) = Izz; |
85 |
dAtomType->setI(inertialMat); |
86 |
|
87 |
} |
88 |
|
89 |
} |
90 |
|
91 |
} //end namespace oopse |