1 // ******************************************************************************
2 //
3 // Title: Force Field X.
4 // Description: Force Field X - Software for Molecular Biophysics.
5 // Copyright: Copyright (c) Michael J. Schnieders 2001-2024.
6 //
7 // This file is part of Force Field X.
8 //
9 // Force Field X is free software; you can redistribute it and/or modify it
10 // under the terms of the GNU General Public License version 3 as published by
11 // the Free Software Foundation.
12 //
13 // Force Field X is distributed in the hope that it will be useful, but WITHOUT
14 // ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
15 // FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
16 // details.
17 //
18 // You should have received a copy of the GNU General Public License along with
19 // Force Field X; if not, write to the Free Software Foundation, Inc., 59 Temple
20 // Place, Suite 330, Boston, MA 02111-1307 USA
21 //
22 // Linking this library statically or dynamically with other modules is making a
23 // combined work based on this library. Thus, the terms and conditions of the
24 // GNU General Public License cover the whole combination.
25 //
26 // As a special exception, the copyright holders of this library give you
27 // permission to link this library with independent modules to produce an
28 // executable, regardless of the license terms of these independent modules, and
29 // to copy and distribute the resulting executable under terms of your choice,
30 // provided that you also meet, for each linked independent module, the terms
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32 // module which is not derived from or based on this library. If you modify this
33 // library, you may extend this exception to your version of the library, but
34 // you are not obligated to do so. If you do not wish to do so, delete this
35 // exception statement from your version.
36 //
37 // ******************************************************************************
38 package ffx.algorithms.mc;
39
40 import static java.lang.String.format;
41
42 import ffx.numerics.Potential;
43 import ffx.potential.AssemblyState;
44 import ffx.potential.MolecularAssembly;
45 import java.util.logging.Logger;
46
47 /**
48 * The MolecularMC class is a framework to take Monte Carlo steps on a molecular system. It does not
49 * implement an MC algorithm, nor does it implement move sets; it is used to evaluate a single MC
50 * step with movements defined by implementations of MCMove.
51 *
52 * @author Michael J. Schnieders
53 * @author Jacob M. Litman
54 * @since 1.0
55 */
56 public class MolecularMC extends BoltzmannMC {
57
58 private static final Logger logger = Logger.getLogger(MolecularMC.class.getName());
59
60 /** The MolecularAssembly to operate on. */
61 private final MolecularAssembly molecularAssembly;
62
63 /** The potential energy for the molecular assembly. */
64 private final Potential potential;
65
66 /** Atomic coordinates. */
67 private double[] x;
68
69 /** Initial state of the MolecularAssembly. */
70 private AssemblyState initialState;
71
72 /**
73 * Constructs a DefaultMC instance with a molecular assembly and its PotentialEnergy. Fancy
74 * footwork will be required if we ever need to use multiple assemblies at once.
75 *
76 * @param molecularAssembly MolecularAssembly to operate on.
77 */
78 public MolecularMC(MolecularAssembly molecularAssembly) {
79 this(molecularAssembly, molecularAssembly.getPotentialEnergy());
80 }
81
82 /**
83 * Constructs a DefaultMC instance with a molecular assembly and a specific Potential.
84 *
85 * @param molecularAssembly MolecularAssembly to operate on.
86 * @param potential a {@link ffx.numerics.Potential} object.
87 */
88 public MolecularMC(MolecularAssembly molecularAssembly, Potential potential) {
89 this.molecularAssembly = molecularAssembly;
90 this.potential = potential;
91 }
92
93 /**
94 * Returns the associated MolecularAssembly.
95 *
96 * @return MolecularAssembly
97 */
98 public MolecularAssembly getMolecularAssembly() {
99 return molecularAssembly;
100 }
101
102 /**
103 * Returns the associated Potential.
104 *
105 * @return Potential.
106 */
107 public Potential getPotential() {
108 return potential;
109 }
110
111 /** {@inheritDoc} */
112 @Override
113 public void revertStep() {
114 initialState.revertState();
115 }
116
117 /** {@inheritDoc} */
118 @Override
119 public String toString() {
120 return "Default Metropolis Monte Carlo implementation\nTemperature: " + getTemperature()
121 + format("\ne1: %10.6f e2: %10.6f\nMolecular Assembly", getE1(), getE2())
122 + molecularAssembly.toString() + "\nPotential: " + potential.toString();
123 }
124
125 /**
126 * {@inheritDoc}
127 *
128 * <p>Calculates the energy at the current state; identical to RotamerOptimization method of same
129 * name.
130 */
131 @Override
132 protected double currentEnergy() {
133 if (x == null) {
134 int nVar = potential.getNumberOfVariables();
135 x = new double[nVar * 3];
136 }
137 try {
138 potential.getCoordinates(x);
139 return potential.energy(x);
140 } catch (ArithmeticException ex) {
141 logger.warning(ex.getMessage());
142 return 1e100;
143 }
144 }
145
146 /** {@inheritDoc} */
147 @Override
148 protected void storeState() {
149 initialState = new AssemblyState(molecularAssembly);
150 }
151 }