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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
31  // and conditions of the license of that module. An independent module is a
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;
39  
40  import ffx.algorithms.dynamics.MolecularDynamics;
41  import ffx.algorithms.dynamics.integrators.IntegratorEnum;
42  import ffx.algorithms.dynamics.thermostats.ThermostatEnum;
43  import ffx.algorithms.optimize.Minimize;
44  import ffx.numerics.Potential;
45  import ffx.potential.MolecularAssembly;
46  import ffx.potential.utils.PotentialsUtils;
47  
48  import java.io.File;
49  import java.util.logging.Logger;
50  
51  /**
52   * AlgorithmUtils, on top of the core functionality of PotentialsUtils, implements additional
53   * functionality such as molecular dynamics and L-BFGS local optimization. This implementation does
54   * not do anything on top of what is specified by the interface, and is used primarily by tests. It
55   * is also potentially useful for third parties who would like to use FFX without its graphical user
56   * interface.
57   *
58   * @author Jacob M. Litman
59   * @author Michael J. Schnieders
60   */
61  public class AlgorithmUtils extends PotentialsUtils implements AlgorithmFunctions {
62  
63    private static final Logger logger = Logger.getLogger(AlgorithmUtils.class.getName());
64    private final long initTime;
65    private long interTime;
66  
67    /** Constructor for AlgorithmUtils. */
68    public AlgorithmUtils() {
69      initTime = System.nanoTime();
70      interTime = initTime;
71    }
72  
73    /**
74     * {@inheritDoc}
75     *
76     * <p>Performs molecular dynamics on a MolecularAssembly.
77     */
78    @Override
79    public void md(MolecularAssembly assembly, int nStep, double timeStep, double printInterval,
80        double saveInterval, double temperature, boolean initVelocities, File dyn) {
81      if (assembly == null) {
82        logger.info(" No active system to minimize.");
83      } else {
84        MolecularDynamics molecularDynamics = new MolecularDynamics(assembly,
85            assembly.getPotentialEnergy(), null, ThermostatEnum.BUSSI, IntegratorEnum.BEEMAN);
86        molecularDynamics.dynamic(nStep, timeStep, printInterval, saveInterval, temperature,
87            initVelocities, dyn);
88      }
89    }
90  
91    /**
92     * {@inheritDoc}
93     *
94     * <p>Minimizes a MolecularAssembly using AMOEBA potential energy.
95     */
96    @Override
97    public Potential minimize(MolecularAssembly assembly, double eps) {
98      if (assembly == null) {
99        logger.info(" No active system to minimize.");
100       return null;
101     } else {
102       Minimize minimize = new Minimize(assembly, null);
103       return minimize.minimize(eps);
104     }
105   }
106 
107   /**
108    * {@inheritDoc}
109    *
110    * <p>Logs time since this interface was created and the last time this method was called. May be
111    * more elegant to replace this by using protected variables and simply inheriting the time()
112    * function.
113    */
114   @Override
115   public double time() {
116     long currTime = System.nanoTime();
117     logger.info(
118         String.format(" Time since interface established: %f", (currTime - initTime) * 1.0E-9));
119     double elapsed = (currTime - interTime) * 1.0E-9;
120     interTime = currTime;
121     logger.info(String.format(" Time since last timer call: %f", elapsed));
122     return elapsed;
123   }
124 }