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.numerics;
39
40 /**
41 * Defines a set of geometric constraints that must be applied self-consistently.
42 *
43 * @author Jacob M. Litman
44 * @author Michael J. Schnieders
45 * @since 1.0
46 */
47 public interface Constraint {
48
49 /**
50 * Applies this Constraint in the context of a partially calculated MD time-step. All arrays are
51 * globally indexed (i.e. includes all system atoms, not just the constrained ones).
52 *
53 * <p>If there is no prior step (e.g. a newly loaded system that has not yet been rigidified),
54 * xPrior and xNew can be copies of each other when passed to the method.
55 *
56 * <p>xPrior corresponds to atomCoordinates in the OpenMM constraint code. Ours will be in
57 * Angstroms, not nm. xNew corresponds to atomCoordinatesP in the OpenMM constraint code. Ours will
58 * be in Angstroms, not nm.
59 *
60 * @param xPrior Atomic coordinates prior to the time-step to be constrained.
61 * @param xNew Atomic coordinates after the time-step; updated in-place to satisfy the
62 * constraint.
63 * @param masses Masses.
64 * @param tol Acceptable constraint tolerance for numerical methods, as a fraction of bond
65 * length.
66 */
67 void applyConstraintToStep(final double[] xPrior, double[] xNew, final double[] masses, double tol);
68
69 /**
70 * Applies this Constraint to velocities, ensuring relative velocities are perpendicular to
71 * constrained bonds, etc., without affecting positions. All arrays are globally indexed (i.e.
72 * includes all system atoms, not just the constrained ones).
73 *
74 * <p>Our positions will be in Angstroms, and velocities in Angstroms/ps, compared to the OpenMM
75 * nm and nm/ps.
76 *
77 * @param x Atomic coordinates (unchanged).
78 * @param v Velocities (updated in-place to satisfy constraints).
79 * @param masses Masses.
80 * @param tol Acceptable constraint tolerance for numerical methods; likely in Angstroms/ps
81 */
82 void applyConstraintToVelocities(final double[] x, double[] v, final double[] masses, double tol);
83
84 /**
85 * Returns the atomic XYZ indices of all Atoms constrained. Guaranteed to be unique. The primary
86 * assumption will be that variables are in sets of 3x Cartesian coordinates.
87 *
88 * @return All indices of constrained Atoms.
89 */
90 int[] constrainedAtomIndices();
91
92 /**
93 * Checks if this Constraint is satisfied.
94 *
95 * @param x Input coordinates to check.
96 * @param tol Numerical tolerance as a fraction of bond stretch.
97 * @return Whether this Constraint is satisfied.
98 */
99 boolean constraintSatisfied(final double[] x, double tol);
100
101 /**
102 * Checks if this Constraint is satisfied. Also checks velocities; bond constraints, for example,
103 * require that relative velocity be orthogonal to the bond. If the velocities vector is null or
104 * the tolerance is zero, velocity checks are skipped.
105 *
106 * @param x Input coordinates to check.
107 * @param v Input velocities to check. If null, velocity check disabled.
108 * @param xTol Numerical tolerance for bond lengths.
109 * @param vTol Numerical tolerance for velocity checks (typically in degrees). If zero,
110 * velocity check disabled.
111 * @return Whether this Constraint is satisfied.
112 */
113 boolean constraintSatisfied(final double[] x, final double[] v, double xTol, double vTol);
114
115 /**
116 * Returns the number of degrees of freedom this Constraint constrains.
117 *
118 * @return Number of frozen DoF.
119 */
120 int getNumDegreesFrozen();
121 }