NAMD
Macros | Functions
ComputeNonbondedFEP.C File Reference
#include "ComputeNonbondedInl.h"
#include "ComputeNonbondedAlch.h"
#include "ComputeNonbondedBase.h"

Go to the source code of this file.

Macros

#define FEPFLAG
 
#define CALCENERGY
 
#define NBTYPE   NBPAIR
 
#define FULLELECT
 
#define MERGEELECT
 
#define SLOWONLY
 
#define NBTYPE   NBSELF
 
#define FULLELECT
 
#define MERGEELECT
 
#define SLOWONLY
 

Functions

void fep_vdw_forceandenergies (BigReal A, BigReal B, BigReal r2, BigReal myVdwShift, BigReal myVdwShift2, BigReal switchdist2, BigReal cutoff2, BigReal switchfactor, Bool vdwForceSwitching, BigReal myVdwLambda, BigReal myVdwLambda2, Bool alchWCAOn, BigReal myRepLambda, BigReal myRepLambda2, BigReal *alch_vdw_energy, BigReal *alch_vdw_force, BigReal *alch_vdw_energy_2)
 

Macro Definition Documentation

◆ CALCENERGY

#define CALCENERGY

Definition at line 170 of file ComputeNonbondedFEP.C.

◆ FEPFLAG

#define FEPFLAG

Definition at line 169 of file ComputeNonbondedFEP.C.

◆ FULLELECT [1/2]

#define FULLELECT

Definition at line 187 of file ComputeNonbondedFEP.C.

◆ FULLELECT [2/2]

#define FULLELECT

Definition at line 187 of file ComputeNonbondedFEP.C.

◆ MERGEELECT [1/2]

#define MERGEELECT

Definition at line 189 of file ComputeNonbondedFEP.C.

◆ MERGEELECT [2/2]

#define MERGEELECT

Definition at line 189 of file ComputeNonbondedFEP.C.

◆ NBTYPE [1/2]

#define NBTYPE   NBPAIR

Definition at line 185 of file ComputeNonbondedFEP.C.

◆ NBTYPE [2/2]

#define NBTYPE   NBSELF

Definition at line 185 of file ComputeNonbondedFEP.C.

◆ SLOWONLY [1/2]

#define SLOWONLY

Definition at line 192 of file ComputeNonbondedFEP.C.

◆ SLOWONLY [2/2]

#define SLOWONLY

Definition at line 192 of file ComputeNonbondedFEP.C.

Function Documentation

◆ fep_vdw_forceandenergies()

void fep_vdw_forceandenergies ( BigReal  A,
BigReal  B,
BigReal  r2,
BigReal  myVdwShift,
BigReal  myVdwShift2,
BigReal  switchdist2,
BigReal  cutoff2,
BigReal  switchfactor,
Bool  vdwForceSwitching,
BigReal  myVdwLambda,
BigReal  myVdwLambda2,
Bool  alchWCAOn,
BigReal  myRepLambda,
BigReal  myRepLambda2,
BigReal *  alch_vdw_energy,
BigReal *  alch_vdw_force,
BigReal *  alch_vdw_energy_2 
)
inline

Copyright (c) 1995, 1996, 1997, 1998, 1999, 2000 by The Board of Trustees of the University of Illinois. All rights reserved.

Definition at line 17 of file ComputeNonbondedFEP.C.

References vdw_energy(), vdw_forceandenergy(), vdw_fswitch_energy(), vdw_fswitch_forceandenergy(), vdw_fswitch_shift(), and vdw_switch().

22  {
23  BigReal U, F, U_2, dU, dU_2, switchmul, switchmul2;
24  /*
25  * The variable naming here is unavoidably awful. A number immediately after
26  * a variable implies a distance to that power. The suffix "_2" indicates an
27  * evaluation at alchLambda2. The prefix "inv" means the inverse (previously
28  * this also used underscores - it was awful).
29  */
30  if (alchWCAOn) {
31  // WCA-on, auxilliary, lambda-dependent cutoff based on Rmin
32  //
33  // Avoid divide by zero - corectly zeroes interaction below.
34  const BigReal Rmin2 = (B <= 0.0 ? 0.0 : powf(2.0*A/B, 1.f/3));
35  if (myRepLambda < 1.0) {
36  // modified repulsive soft-core
37  // All of the scaling is baked into the shift and cutoff values. There
38  // are no linear coupling terms out front.
39  const BigReal WCAshift = Rmin2*(1 - myRepLambda)*(1 - myRepLambda);
40  if (r2 <= Rmin2 - WCAshift) {
41  const BigReal epsilon = B*B/(4.0*A);
42  vdw_forceandenergy(A, B, r2 + WCAshift, &U, &F);
43  *alch_vdw_energy = U + epsilon;
44  *alch_vdw_force = F;
45  } else {
46  *alch_vdw_energy = 0.0;
47  *alch_vdw_force = 0.0;
48  }
49  } else { // myRepLambda == 1.0
50  if (vdwForceSwitching) {
51  // force and potential switching
52  if (r2 <= Rmin2) {
53  // normal LJ, potential w/two shifts
54  const BigReal epsilon = B*B/(4.0*A);
55  vdw_fswitch_shift(A, B, switchdist2, cutoff2, &dU);
56  vdw_forceandenergy(A, B, r2, &U, &F);
57  *alch_vdw_energy = U + (1 - myVdwLambda)*epsilon + myVdwLambda*dU;
58  *alch_vdw_force = F;
59  } else if (r2 <= switchdist2) {
60  // normal LJ potential w/shift
61  vdw_fswitch_shift(A, B, switchdist2, cutoff2, &dU);
62  vdw_forceandenergy(A, B, r2, &U, &F);
63  *alch_vdw_energy = myVdwLambda*(U + dU);
64  *alch_vdw_force = myVdwLambda*F;
65  } else { // r2 > switchdist
66  // normal LJ potential with linear coupling
67  vdw_fswitch_forceandenergy(A, B, r2, switchdist2, cutoff2, &U, &F);
68  *alch_vdw_energy = myVdwLambda*U;
69  *alch_vdw_force = myVdwLambda*F;
70  }
71  } else {
72  // potential switching - also correct for no switching
73  if (r2 <= Rmin2) {
74  // normal LJ potential w/shift
75  const BigReal epsilon = B*B/(4.0*A);
76  vdw_forceandenergy(A, B, r2, &U, &F);
77  *alch_vdw_energy = U + (1 - myVdwLambda)*epsilon;
78  *alch_vdw_force = F;
79  } else { // r2 > Rmin2
80  // normal LJ potential with linear coupling
81  vdw_switch(r2, switchdist2, cutoff2, switchfactor, &switchmul, \
82  &switchmul2);
83  vdw_forceandenergy(A, B, r2, &U, &F);
84  *alch_vdw_energy = myVdwLambda*switchmul*U;
85  *alch_vdw_force = myVdwLambda*(switchmul*F + switchmul2*U);
86  }
87  }
88  }
89  if (myRepLambda2 < 1.0) {
90  // Same as above, but energy only. This is done separately bc the
91  // cutoffs are lambda dependent.
92  const BigReal WCAshift_2 = Rmin2*(1 - myRepLambda2)*(1 - myRepLambda2);
93  if (r2 <= Rmin2 - WCAshift_2) {
94  const BigReal epsilon = B*B/(4.0*A);
95  vdw_energy(A, B, r2 + WCAshift_2, &U_2);
96  *alch_vdw_energy_2 = U_2 + epsilon;
97  } else {
98  *alch_vdw_energy_2 = 0.0;
99  }
100  } else { // myRepLambda2 == 1.0
101  if (vdwForceSwitching) {
102  // force and potential switching
103  if (r2 <= Rmin2) {
104  // normal LJ, potential w/two shifts
105  const BigReal epsilon = B*B/(4.0*A);
106  vdw_fswitch_shift(A, B, switchdist2, cutoff2, &dU_2);
107  vdw_energy(A, B, r2, &U_2);
108  *alch_vdw_energy_2 = \
109  U_2 + (1 - myVdwLambda2)*epsilon + myVdwLambda2*dU_2;
110  } else if (r2 <= switchdist2) {
111  // normal LJ potential w/shift
112  vdw_fswitch_shift(A, B, switchdist2, cutoff2, &dU_2);
113  vdw_energy(A, B, r2, &U_2);
114  *alch_vdw_energy_2 = myVdwLambda2*(U_2 + dU_2);
115  } else { // r2 > switchdist
116  vdw_fswitch_energy(A, B, r2, switchdist2, cutoff2, &U_2);
117  *alch_vdw_energy_2 = myVdwLambda2*U_2;
118  }
119  } else {
120  // potential switching - also correct for no switching
121  if (r2 <= Rmin2) {
122  // normal LJ potential w/shift
123  const BigReal epsilon = B*B/(4.0*A);
124  vdw_energy(A, B, r2, &U_2);
125  *alch_vdw_energy_2 = U_2 + (1 - myVdwLambda2)*epsilon;
126  } else { // r2 > Rmin2
127  // normal LJ potential with linear coupling
128  vdw_switch(r2, switchdist2, cutoff2, switchfactor, &switchmul, \
129  &switchmul2);
130  vdw_energy(A, B, r2, &U_2);
131  *alch_vdw_energy_2 = myVdwLambda2*switchmul*U_2;
132  }
133  }
134  }
135  } else { // WCA-off
136  if (vdwForceSwitching) {
137  // force and potential switching
138  if (r2 <= switchdist2) {
139  // normal LJ potential w/shift
140  vdw_forceandenergy(A, B, r2 + myVdwShift, &U, &F);
141  vdw_fswitch_shift(A, B, switchdist2 + myVdwShift, cutoff2, &dU);
142  vdw_energy(A, B, r2 + myVdwShift2, &U_2);
143  vdw_fswitch_shift(A, B, switchdist2 + myVdwShift2, cutoff2, &dU_2);
144  *alch_vdw_energy = myVdwLambda*(U + dU);
145  *alch_vdw_energy_2 = myVdwLambda2*(U_2 + dU_2);
146  *alch_vdw_force = myVdwLambda*F;
147  } else { // r2 > switchdist2
148  vdw_fswitch_forceandenergy(A, B, r2 + myVdwShift, \
149  switchdist2 + myVdwShift, cutoff2, &U, &F);
150  vdw_fswitch_energy(A, B, r2 + myVdwShift2, switchdist2 + myVdwShift2, \
151  cutoff2, &U_2);
152  *alch_vdw_energy = myVdwLambda*U;
153  *alch_vdw_energy_2 = myVdwLambda2*U_2;
154  *alch_vdw_force = myVdwLambda*F;
155  }
156  } else {
157  // potential switching - also correct for no switching
158  vdw_switch(r2, switchdist2, cutoff2, switchfactor, &switchmul, \
159  &switchmul2);
160  vdw_forceandenergy(A, B, r2 + myVdwShift, &U, &F);
161  vdw_energy(A, B, r2 + myVdwShift2, &U_2);
162  *alch_vdw_energy = myVdwLambda*switchmul*U;
163  *alch_vdw_energy_2 = myVdwLambda2*switchmul*U_2;
164  *alch_vdw_force = myVdwLambda*(switchmul*F + switchmul2*U);
165  }
166  }
167 }
vdw_fswitch_energy
void vdw_fswitch_energy(const BigReal A, const BigReal B, const BigReal r2, const BigReal switchdist2, const BigReal cutoff2, BigReal *U)
Definition: ComputeNonbondedAlch.h:75
vdw_forceandenergy
void vdw_forceandenergy(const BigReal A, const BigReal B, const BigReal r2, BigReal *U, BigReal *F)
Definition: ComputeNonbondedAlch.h:16
vdw_switch
void vdw_switch(const BigReal r2, const BigReal switchdist2, const BigReal cutoff2, const BigReal switchfactor, BigReal *switchmul, BigReal *switchmul2)
Definition: ComputeNonbondedAlch.h:35
vdw_fswitch_forceandenergy
void vdw_fswitch_forceandenergy(const BigReal A, const BigReal B, const BigReal r2, const BigReal switchdist2, const BigReal cutoff2, BigReal *U, BigReal *F)
Definition: ComputeNonbondedAlch.h:56
vdw_energy
void vdw_energy(const BigReal A, const BigReal B, const BigReal r2, BigReal *U)
Definition: ComputeNonbondedAlch.h:25
vdw_fswitch_shift
void vdw_fswitch_shift(const BigReal A, const BigReal B, const BigReal switchdist2, const BigReal cutoff2, BigReal *dU)
Definition: ComputeNonbondedAlch.h:97
BigReal
double BigReal
Definition: common.h:123
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