src/rnemd/RNEMDParameters.cpp

/*
 * Copyright (c) 2012 The University of Notre Dame. All Rights Reserved.
 *
 * The University of Notre Dame grants you ("Licensee") a
 * non-exclusive, royalty free, license to use, modify and
 * redistribute this software in source and binary code form, provided
 * that the following conditions are met:
 *
 * 1. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 2. Redistributions in binary form must reproduce the above copyright
 *    notice, this list of conditions and the following disclaimer in the
 *    documentation and/or other materials provided with the
 *    distribution.
 *
 * This software is provided "AS IS," without a warranty of any
 * kind. All express or implied conditions, representations and
 * warranties, including any implied warranty of merchantability,
 * fitness for a particular purpose or non-infringement, are hereby
 * excluded.  The University of Notre Dame and its licensors shall not
 * be liable for any damages suffered by licensee as a result of
 * using, modifying or distributing the software or its
 * derivatives. In no event will the University of Notre Dame or its
 * licensors be liable for any lost revenue, profit or data, or for
 * direct, indirect, special, consequential, incidental or punitive
 * damages, however caused and regardless of the theory of liability,
 * arising out of the use of or inability to use software, even if the
 * University of Notre Dame has been advised of the possibility of
 * such damages.
 *
 * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
 * research, please cite the appropriate papers when you publish your
 * work.  Good starting points are:
 *                                                                      
 * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).             
 * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
 * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).          
 * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
 * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 */
 
#include <iostream>
#include <stdlib.h>
#include <string.h>

#include "rnemd/RNEMDParameters.hpp"

namespace OpenMD {
  RNEMDParameters::RNEMDParameters() { 
    DefineOptionalParameterWithDefaultValue(UseRNEMD, "useRNEMD", false);
    DefineOptionalParameterWithDefaultValue(ObjectSelection, "objectSelection", "select all");
    DefineOptionalParameterWithDefaultValue(Method, "method", "VSS");
    DefineOptionalParameter(FluxType, "fluxType");

    DefineOptionalParameterWithDefaultValue(ExchangeTime, "exchangeTime", 100.0);
    DefineOptionalParameter(KineticFlux, "kineticFlux");
    DefineOptionalParameter(MomentumFlux, "momentumFlux");
    DefineOptionalParameter(MomentumFluxVector, "momentumFluxVector");
    DefineOptionalParameter(AngularMomentumFlux, "angularMomentumFlux");
    DefineOptionalParameter(AngularMomentumFluxVector, 
                            "angularMomentumFluxVector");    
    DefineOptionalParameter(SlabWidth, "slabWidth");
    DefineOptionalParameter(SlabACenter, "slabAcenter");
    DefineOptionalParameter(SlabBCenter, "slabBcenter");
    DefineOptionalParameter(SphereARadius, "sphereAradius");
    DefineOptionalParameter(SphereBRadius, "sphereBradius");    
    DefineOptionalParameter(SelectionA, "selectionA");
    DefineOptionalParameter(SelectionB, "selectionB");
    DefineOptionalParameter(CoordinateOrigin, "coordinateOrigin");
    DefineOptionalParameter(OutputFileName, "outputFileName");
    DefineOptionalParameterWithDefaultValue(OutputBins, "outputBins", 20);
    DefineOptionalParameterWithDefaultValue(OutputBinWidth, "outputBinWidth", 2.0);
    DefineOptionalParameter(OutputFields, "outputFields");
  }
  
  RNEMDParameters::~RNEMDParameters() {    
  }
  
  void RNEMDParameters::validate() {
    CheckParameter(ExchangeTime, isPositive());
    CheckParameter(OutputBins, isPositive());
    CheckParameter(OutputBinWidth, isPositive());
    CheckParameter(Method, 
                   isEqualIgnoreCase("swap") ||  
                   isEqualIgnoreCase("NIVS")  ||
                   isEqualIgnoreCase("VSS"));
    CheckParameter(FluxType, 
                   isEqualIgnoreCase("KE") ||
                   isEqualIgnoreCase("Px") ||
                   isEqualIgnoreCase("Py") ||
                   isEqualIgnoreCase("Pz") ||
                   isEqualIgnoreCase("Lx") ||
                   isEqualIgnoreCase("Ly") ||
                   isEqualIgnoreCase("Lz") ||
                   isEqualIgnoreCase("Pvector") ||
                   isEqualIgnoreCase("Lvector") ||
                   isEqualIgnoreCase("KE+Px") || 
                   isEqualIgnoreCase("KE+Py") || 
                   isEqualIgnoreCase("KE+Lx") || 
                   isEqualIgnoreCase("KE+Ly") || 
                   isEqualIgnoreCase("KE+Lz") || 
                   isEqualIgnoreCase("KE+Pvector") ||
                   isEqualIgnoreCase("KE+Lvector")
                   );
  }
  
}
Revision:	1854
Committed:	Thu Mar 28 20:54:06 2013 UTC (12 years, 6 months ago) by gezelter
File size:	5096 byte(s)
Log Message:	First pass at angular momentum aware version of VSS-RNEMD.
#	User	Rev	Content
1	gezelter	1731	/*
2			* Copyright (c) 2012 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. Redistributions of source code must retain the above copyright
10			* notice, this list of conditions and the following disclaimer.
11			*
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.
16			*
17			* This software is provided "AS IS," without a warranty of any
18			* kind. All express or implied conditions, representations and
19			* warranties, including any implied warranty of merchantability,
20			* fitness for a particular purpose or non-infringement, are hereby
21			* excluded. The University of Notre Dame and its licensors shall not
22			* be liable for any damages suffered by licensee as a result of
23			* using, modifying or distributing the software or its
24			* derivatives. In no event will the University of Notre Dame or its
25			* licensors be liable for any lost revenue, profit or data, or for
26			* direct, indirect, special, consequential, incidental or punitive
27			* damages, however caused and regardless of the theory of liability,
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	gezelter	1850	* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
39	gezelter	1731	* [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 <iostream>
44			#include <stdlib.h>
45			#include <string.h>
46
47			#include "rnemd/RNEMDParameters.hpp"
48
49			namespace OpenMD {
50			RNEMDParameters::RNEMDParameters() {
51			DefineOptionalParameterWithDefaultValue(UseRNEMD, "useRNEMD", false);
52	gezelter	1773	DefineOptionalParameterWithDefaultValue(ObjectSelection, "objectSelection", "select all");
53			DefineOptionalParameterWithDefaultValue(Method, "method", "VSS");
54			DefineOptionalParameter(FluxType, "fluxType");
55
56	gezelter	1731	DefineOptionalParameterWithDefaultValue(ExchangeTime, "exchangeTime", 100.0);
57	gezelter	1773	DefineOptionalParameter(KineticFlux, "kineticFlux");
58			DefineOptionalParameter(MomentumFlux, "momentumFlux");
59			DefineOptionalParameter(MomentumFluxVector, "momentumFluxVector");
60	gezelter	1854	DefineOptionalParameter(AngularMomentumFlux, "angularMomentumFlux");
61			DefineOptionalParameter(AngularMomentumFluxVector,
62			"angularMomentumFluxVector");
63	gezelter	1773	DefineOptionalParameter(SlabWidth, "slabWidth");
64			DefineOptionalParameter(SlabACenter, "slabAcenter");
65			DefineOptionalParameter(SlabBCenter, "slabBcenter");
66	gezelter	1854	DefineOptionalParameter(SphereARadius, "sphereAradius");
67			DefineOptionalParameter(SphereBRadius, "sphereBradius");
68			DefineOptionalParameter(SelectionA, "selectionA");
69			DefineOptionalParameter(SelectionB, "selectionB");
70			DefineOptionalParameter(CoordinateOrigin, "coordinateOrigin");
71	gezelter	1773	DefineOptionalParameter(OutputFileName, "outputFileName");
72			DefineOptionalParameterWithDefaultValue(OutputBins, "outputBins", 20);
73	gezelter	1854	DefineOptionalParameterWithDefaultValue(OutputBinWidth, "outputBinWidth", 2.0);
74			DefineOptionalParameter(OutputFields, "outputFields");
75	gezelter	1731	}
76
77			RNEMDParameters::~RNEMDParameters() {
78			}
79
80			void RNEMDParameters::validate() {
81			CheckParameter(ExchangeTime, isPositive());
82	gezelter	1773	CheckParameter(OutputBins, isPositive());
83	gezelter	1854	CheckParameter(OutputBinWidth, isPositive());
84	gezelter	1773	CheckParameter(Method,
85			isEqualIgnoreCase("swap") \|\|
86			isEqualIgnoreCase("NIVS") \|\|
87			isEqualIgnoreCase("VSS"));
88			CheckParameter(FluxType,
89	gezelter	1854	isEqualIgnoreCase("KE") \|\|
90	gezelter	1773	isEqualIgnoreCase("Px") \|\|
91			isEqualIgnoreCase("Py") \|\|
92			isEqualIgnoreCase("Pz") \|\|
93	gezelter	1854	isEqualIgnoreCase("Lx") \|\|
94			isEqualIgnoreCase("Ly") \|\|
95			isEqualIgnoreCase("Lz") \|\|
96	gezelter	1773	isEqualIgnoreCase("Pvector") \|\|
97	gezelter	1854	isEqualIgnoreCase("Lvector") \|\|
98	gezelter	1773	isEqualIgnoreCase("KE+Px") \|\|
99			isEqualIgnoreCase("KE+Py") \|\|
100	gezelter	1854	isEqualIgnoreCase("KE+Lx") \|\|
101			isEqualIgnoreCase("KE+Ly") \|\|
102			isEqualIgnoreCase("KE+Lz") \|\|
103			isEqualIgnoreCase("KE+Pvector") \|\|
104			isEqualIgnoreCase("KE+Lvector")
105			);
106	gezelter	1731	}
107
108			}