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.numerics.Potential;
41 import ffx.potential.MolecularAssembly;
42 import ffx.potential.utils.PotentialsFunctions;
43 import java.io.File;
44
45 /**
46 * AlgorithmFunctions, on top of the core functionality of PotentialsFunctions, describes additional
47 * functionality such as molecular dynamics and L-BFGS local optimization.
48 *
49 * <p>This is implemented in two locations: UIUtils in the User Interfaces package, and in
50 * AlgorithmsUtils in the Algorithm package.
51 *
52 * <p>The UIUtils implementation is the default for Force Field X; on top of the core functionality,
53 * it also updates the FFX graphical user interface and tree structure.
54 *
55 * <p>The AlgorithmUtils implementation lacks the extra functionality of the UIUtils implementation,
56 * and simply accomplishes the required task. This is used by our tests, and is also potentially
57 * useful for third parties who would like to use FFX without its GUI.
58 *
59 * @author Jacob M. Litman
60 * @author Michael J. Schnieders
61 */
62 public interface AlgorithmFunctions extends PotentialsFunctions {
63
64 /**
65 * Returns a default Listener if available (null by default).
66 *
67 * @return An AlgorithmListener or null.
68 */
69 default AlgorithmListener getDefaultListener() {
70 return null;
71 }
72
73 /**
74 * Runs molecular dynamics on an assembly.
75 *
76 * @param assembly a {@link ffx.potential.MolecularAssembly} object.
77 * @param nStep Timesteps
78 * @param timeStep Time per step
79 * @param printInterval a double.
80 * @param saveInterval a double.
81 * @param temperature a double.
82 * @param initVelocities Initialize velocities from Maxwell-Boltzmann distribution
83 * @param dyn Dynamics file
84 */
85 void md(
86 MolecularAssembly assembly,
87 int nStep,
88 double timeStep,
89 double printInterval,
90 double saveInterval,
91 double temperature,
92 boolean initVelocities,
93 File dyn);
94
95 /**
96 * Relax the coordinates of a MolecularAssembly and minimize its potential energy
97 *
98 * @param assembly a {@link ffx.potential.MolecularAssembly} object.
99 * @param eps RMS gradient convergence criteria
100 * @return A <code>Potential</code>
101 */
102 Potential minimize(MolecularAssembly assembly, double eps);
103 }