1 // ******************************************************************************
2 //
3 // Title: Force Field X.
4 // Description: Force Field X - Software for Molecular Biophysics.
5 // Copyright: Copyright (c) Michael J. Schnieders 2001-2025.
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
44 import java.io.File;
45
46 /**
47 * AlgorithmFunctions, on top of the core functionality of PotentialsFunctions, describes additional
48 * functionality such as molecular dynamics and L-BFGS local optimization.
49 *
50 * <p>This is implemented in two locations: UIUtils in the User Interfaces package, and in
51 * AlgorithmsUtils in the Algorithm package.
52 *
53 * <p>The UIUtils implementation is the default for Force Field X; on top of the core functionality,
54 * it also updates the FFX graphical user interface and tree structure.
55 *
56 * <p>The AlgorithmUtils implementation lacks the extra functionality of the UIUtils implementation,
57 * and simply accomplishes the required task. This is used by our tests, and is also potentially
58 * useful for third parties who would like to use FFX without its GUI.
59 *
60 * @author Jacob M. Litman
61 * @author Michael J. Schnieders
62 */
63 public interface AlgorithmFunctions extends PotentialsFunctions {
64
65 /**
66 * Returns a default Listener if available (null by default).
67 *
68 * @return An AlgorithmListener or null.
69 */
70 default AlgorithmListener getDefaultListener() {
71 return null;
72 }
73
74 /**
75 * Runs molecular dynamics on an assembly.
76 *
77 * @param assembly a {@link ffx.potential.MolecularAssembly} object.
78 * @param nStep Timesteps
79 * @param timeStep Time per step
80 * @param printInterval a double.
81 * @param saveInterval a double.
82 * @param temperature a double.
83 * @param initVelocities Initialize velocities from Maxwell-Boltzmann distribution
84 * @param dyn Dynamics file
85 */
86 void md(
87 MolecularAssembly assembly,
88 int nStep,
89 double timeStep,
90 double printInterval,
91 double saveInterval,
92 double temperature,
93 boolean initVelocities,
94 File dyn);
95
96 /**
97 * Relax the coordinates of a MolecularAssembly and minimize its potential energy
98 *
99 * @param assembly a {@link ffx.potential.MolecularAssembly} object.
100 * @param eps RMS gradient convergence criteria
101 * @return A <code>Potential</code>
102 */
103 Potential minimize(MolecularAssembly assembly, double eps);
104 }