src/perturbations/UniformGradient.hpp

/*
 * Copyright (c) 2014 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).
 */
 

/*! \file perturbations/UniformGradient.hpp
    \brief Uniform Electric Field Gradient perturbation
*/

#ifndef PERTURBATIONS_UNIFORMGRADIENT_HPP
#define PERTURBATIONS_UNIFORMGRADIENT_HPP

#include "perturbations/Perturbation.hpp"
#include "brains/SimInfo.hpp"

namespace OpenMD {
   
  //! Applies a uniform electric field gradient to the system
  /*! The gradient is applied as an external perturbation.  The user specifies

  \code{.unparsed}
    uniformGradientStrength = c;
    uniformGradientDirection1 = (a1, a2, a3)
    uniformGradientDirection2 = (b1, b2, b3);
  \endcode 
    
    in the .md file where the two direction vectors, \f$ \mathbf{a} \f$ 
    and \f$ \mathbf{b} \f$ are unit vectors, and the value of \f$ g \f$ 
    is in units of \f$ V / \AA^2 \f$

    The electrostatic potential corresponding to this uniform gradient is

    \f$ \phi(\mathbf{r})  = - \frac{g}{2} \left[ 
    \left(a_1 b_1 - \frac{\cos\psi}{3}\right) x^2
    + (a_1 b_2 + a_2 b_1) x y + (a_1 b_3 + a_3 b_1) x z +
    + (a_2 b_1 + a_1 b_2) y x 
    + \left(a_2 b_2 - \frac{\cos\psi}{3}\right) y^2
    + (a_2 b_3 + a_3 b_2) y z + (a_3 b_1 + a_1 b_3) z x 
    + (a_3 b_2 + a_2 b_3) z y
    + \left(a_3 b_3 - \frac{\cos\psi}{3}\right) z^2 \right] \f$

    where \f$ \cos \psi = \mathbf{a} \cdot \mathbf{b} \f$.  Note that
    this potential grows unbounded and is not periodic.  For these reasons,
    care should be taken in using a Uniform Gradient with point charges.

    The corresponding field is:

    \f$ \mathbf{E} = \frac{g}{2} \left( 
    2\left(a_1 b_1 - \frac{\cos\psi}{3}\right) x +  (a_1 b_2 + a_2 b_1) y 
    + (a_1 b_3 + a_3 b_1) z  \\ 
    (a_2 b_1 + a_1 b_2)  x + 2 \left(a_2 b_2 - \frac{\cos\psi}{3}\right) y 
    + (a_2 b_3 + a_3 b_2) z \\ 
    (a_3 b_1 + a_1 b_3) x +  (a_3 b_2 + a_2 b_3) y 
    + 2 \left(a_3 b_3 - \frac{\cos\psi}{3}\right) z \end{array} \right) \f$

    The field also grows unbounded and is not periodic.  For these reasons,
    care should be taken in using a Uniform Gradient with point dipoles.

    The corresponding field gradient is:

    \f$ \nabla \mathbf{E} = \frac{g}{2} \left( \array{ccc}  
    2\left(a_1 b_1 - \frac{\cos\psi}{3}\right)  &  
    (a_1 b_2 + a_2 b_1) & (a_1 b_3 + a_3 b_1) \\
    (a_2 b_1 + a_1 b_2)  & 2 \left(a_2 b_2 - \frac{\cos\psi}{3}\right) & 
    (a_2 b_3 + a_3 b_2) \\  
    (a_3 b_1 + a_1 b_3) & (a_3 b_2 + a_2 b_3) & 
    2 \left(a_3 b_3 - \frac{\cos\psi}{3}\right) \end{array} \right) \f$

    which is uniform everywhere.

    The uniform field gradient applies a force on charged atoms, 
    \f$ \mathbf{F} = C \mathbf{E}(\mathbf{r}) \f$.  
    For dipolar atoms, the gradient applies both a potential, 
    \f$ U = -\mathbf{D} \cdot \mathbf{E}(\mathbf{r}) \f$, a force, 
    \f$ \mathbf{F} = \mathbf{D} \cdot \nabla \mathbf{E} \f$, and a torque,
    \f$ \mathbf{\tau} = \mathbf{D} \times \mathbf{E}(\mathbf{r}) \f$.
    
    For quadrupolar atoms, the uniform field gradient exerts a potential, 
    \f$ U = - \mathsf{Q}:\nabla \mathbf{E} $\f, and a torque 
    \f$ \mathbf{F} = 2 \mathsf{Q} \times \nabla \mathbf{E} \f$
    
  */ 
  class UniformGradient : public Perturbation {
    

  public:
    UniformGradient(SimInfo* info);
    
  protected:
    virtual void initialize();
    virtual void applyPerturbation();
    
  private:
    bool initialized;
    bool doUniformGradient;
    bool doParticlePot;
    Globals* simParams;
    SimInfo* info_;
    Mat3x3d Grad_;
    Vector3d a_, b_;
    RealType g_, cpsi_;    
  };


} //end namespace OpenMD
#endif

Revision:	2034
Committed:	Mon Nov 3 16:49:03 2014 UTC (11 years ago) by gezelter
File size:	5716 byte(s)
Log Message:	Updating UniformGradient to the new parameter structure (two unit vectors and a gradient strength).
#	User	Rev	Content
1	gezelter	2026	/*
2			* Copyright (c) 2014 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			* [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
44			/*! \file perturbations/UniformGradient.hpp
45			\brief Uniform Electric Field Gradient perturbation
46			*/
47
48			#ifndef PERTURBATIONS_UNIFORMGRADIENT_HPP
49			#define PERTURBATIONS_UNIFORMGRADIENT_HPP
50
51			#include "perturbations/Perturbation.hpp"
52			#include "brains/SimInfo.hpp"
53
54			namespace OpenMD {
55
56			//! Applies a uniform electric field gradient to the system
57			/*! The gradient is applied as an external perturbation. The user specifies
58
59			\code{.unparsed}
60	gezelter	2034	uniformGradientStrength = c;
61			uniformGradientDirection1 = (a1, a2, a3)
62			uniformGradientDirection2 = (b1, b2, b3);
63	gezelter	2026	\endcode
64
65	gezelter	2034	in the .md file where the two direction vectors, \f$ \mathbf{a} \f$
66			and \f$ \mathbf{b} \f$ are unit vectors, and the value of \f$ g \f$
67			is in units of \f$ V / \AA^2 \f$
68	gezelter	2026
69			The electrostatic potential corresponding to this uniform gradient is
70
71	gezelter	2034	\f$ \phi(\mathbf{r}) = - \frac{g}{2} \left[
72			\left(a_1 b_1 - \frac{\cos\psi}{3}\right) x^2
73			+ (a_1 b_2 + a_2 b_1) x y + (a_1 b_3 + a_3 b_1) x z +
74			+ (a_2 b_1 + a_1 b_2) y x
75			+ \left(a_2 b_2 - \frac{\cos\psi}{3}\right) y^2
76			+ (a_2 b_3 + a_3 b_2) y z + (a_3 b_1 + a_1 b_3) z x
77			+ (a_3 b_2 + a_2 b_3) z y
78			+ \left(a_3 b_3 - \frac{\cos\psi}{3}\right) z^2 \right] \f$
79	gezelter	2026
80	gezelter	2034	where \f$ \cos \psi = \mathbf{a} \cdot \mathbf{b} \f$. Note that
81			this potential grows unbounded and is not periodic. For these reasons,
82	gezelter	2026	care should be taken in using a Uniform Gradient with point charges.
83
84			The corresponding field is:
85
86	gezelter	2034	\f$ \mathbf{E} = \frac{g}{2} \left(
87			2\left(a_1 b_1 - \frac{\cos\psi}{3}\right) x + (a_1 b_2 + a_2 b_1) y
88			+ (a_1 b_3 + a_3 b_1) z \\
89			(a_2 b_1 + a_1 b_2) x + 2 \left(a_2 b_2 - \frac{\cos\psi}{3}\right) y
90			+ (a_2 b_3 + a_3 b_2) z \\
91			(a_3 b_1 + a_1 b_3) x + (a_3 b_2 + a_2 b_3) y
92			+ 2 \left(a_3 b_3 - \frac{\cos\psi}{3}\right) z \end{array} \right) \f$
93	gezelter	2026
94			The field also grows unbounded and is not periodic. For these reasons,
95			care should be taken in using a Uniform Gradient with point dipoles.
96
97			The corresponding field gradient is:
98
99	gezelter	2034	\f$ \nabla \mathbf{E} = \frac{g}{2} \left( \array{ccc}
100			2\left(a_1 b_1 - \frac{\cos\psi}{3}\right) &
101			(a_1 b_2 + a_2 b_1) & (a_1 b_3 + a_3 b_1) \\
102			(a_2 b_1 + a_1 b_2) & 2 \left(a_2 b_2 - \frac{\cos\psi}{3}\right) &
103			(a_2 b_3 + a_3 b_2) \\
104			(a_3 b_1 + a_1 b_3) & (a_3 b_2 + a_2 b_3) &
105			2 \left(a_3 b_3 - \frac{\cos\psi}{3}\right) \end{array} \right) \f$
106	gezelter	2026
107			which is uniform everywhere.
108
109			The uniform field gradient applies a force on charged atoms,
110			\f$ \mathbf{F} = C \mathbf{E}(\mathbf{r}) \f$.
111			For dipolar atoms, the gradient applies both a potential,
112			\f$ U = -\mathbf{D} \cdot \mathbf{E}(\mathbf{r}) \f$, a force,
113			\f$ \mathbf{F} = \mathbf{D} \cdot \nabla \mathbf{E} \f$, and a torque,
114			\f$ \mathbf{\tau} = \mathbf{D} \times \mathbf{E}(\mathbf{r}) \f$.
115
116			For quadrupolar atoms, the uniform field gradient exerts a potential,
117			\f$ U = - \mathsf{Q}:\nabla \mathbf{E} $\f, and a torque
118			\f$ \mathbf{F} = 2 \mathsf{Q} \times \nabla \mathbf{E} \f$
119
120			*/
121			class UniformGradient : public Perturbation {
122
123
124			public:
125			UniformGradient(SimInfo* info);
126
127			protected:
128			virtual void initialize();
129			virtual void applyPerturbation();
130
131			private:
132			bool initialized;
133			bool doUniformGradient;
134			bool doParticlePot;
135			Globals* simParams;
136			SimInfo* info_;
137			Mat3x3d Grad_;
138	gezelter	2034	Vector3d a_, b_;
139			RealType g_, cpsi_;
140	gezelter	2026	};
141
142
143			} //end namespace OpenMD
144			#endif
145