NAMD
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#include "time.h"
#include <math.h>
#include "charm++.h"
#include "qd.h"
#include "SimParameters.h"
#include "HomePatch.h"
#include "AtomMap.h"
#include "Node.h"
#include "PatchMap.inl"
#include "main.h"
#include "ProxyMgr.decl.h"
#include "ProxyMgr.h"
#include "Migration.h"
#include "Molecule.h"
#include "PatchMgr.h"
#include "Sequencer.h"
#include "Broadcasts.h"
#include "LdbCoordinator.h"
#include "ReductionMgr.h"
#include "Sync.h"
#include "Random.h"
#include "Priorities.h"
#include "ComputeNonbondedUtil.h"
#include "ComputeGBIS.inl"
#include "SortAtoms.h"
#include "ComputeQM.h"
#include "ComputeQMMgr.decl.h"
#include "NamdEventsProfiling.h"
#include "Debug.h"
#include <vector>
#include <algorithm>
#include "ComputeNonbondedMICKernel.h"
Go to the source code of this file.
Macros | |
#define | TINY 1.0e-20; |
#define | MAXHGS 10 |
#define | MIN_DEBUG_LEVEL 2 |
#define | MASS_EPSILON (1.0e-35) |
#define | FIX_FOR_WATER |
Typedefs | |
typedef int | HGArrayInt [MAXHGS] |
typedef BigReal | HGArrayBigReal [MAXHGS] |
typedef zVector | HGArrayVector [MAXHGS] |
typedef BigReal | HGMatrixBigReal [MAXHGS][MAXHGS] |
typedef zVector | HGMatrixVector [MAXHGS][MAXHGS] |
Functions | |
int | average (CompAtom *qtilde, const HGArrayVector &q, BigReal *lambda, const int n, const int m, const HGArrayBigReal &imass, const HGArrayBigReal &length2, const HGArrayInt &ial, const HGArrayInt &ibl, const HGArrayVector &refab, const BigReal tolf, const int ntrial) |
void | mollify (CompAtom *qtilde, const HGArrayVector &q0, const BigReal *lambda, HGArrayVector &force, const int n, const int m, const HGArrayBigReal &imass, const HGArrayInt &ial, const HGArrayInt &ibl, const HGArrayVector &refab) |
static int | compDistance (const void *a, const void *b) |
void | lubksb (HGMatrixBigReal &a, int n, HGArrayInt &indx, HGArrayBigReal &b) |
void | ludcmp (HGMatrixBigReal &a, int n, HGArrayInt &indx, BigReal *d) |
void | G_q (const HGArrayVector &refab, HGMatrixVector &gqij, const int n, const int m, const HGArrayInt &ial, const HGArrayInt &ibl) |
#define FIX_FOR_WATER |
Redistribute forces from lone pair site onto its host atoms.
Atoms are "labeled" i, j, k, l, where atom i is the lone pair. Positions of atoms are ri, rj, rk, rl. Forces of atoms are fi, fj, fk, fl; updated forces are returned. Accumulate updates to the virial.
The forces on the atoms are updated so that:
If "midpt" is true (nonzero), then use the midpoint of rk and rl (e.g. rk and rl are the hydrogen atoms for water). Otherwise use planes defined by ri,rj,rk and rj,rk,rl.
Having "midpt" set true corresponds in CHARMM to having a negative distance parameter in Lphost.
Use FIX_FOR_WATER below to fix the case that occurs when the lone pair site for water lies on the perpendicular bisector of rk and rl, making the cross(r,s) zero.
Definition at line 1404 of file HomePatch.C.
#define MASS_EPSILON (1.0e-35) |
Definition at line 74 of file HomePatch.C.
#define MAXHGS 10 |
Definition at line 52 of file HomePatch.C.
#define MIN_DEBUG_LEVEL 2 |
Definition at line 53 of file HomePatch.C.
#define TINY 1.0e-20; |
Copyright (c) 1995, 1996, 1997, 1998, 1999, 2000 by The Board of Trustees of the University of Illinois. All rights reserved.
Definition at line 51 of file HomePatch.C.
Referenced by ludcmp().
Definition at line 63 of file HomePatch.C.
typedef int HGArrayInt[MAXHGS] |
Definition at line 62 of file HomePatch.C.
Definition at line 64 of file HomePatch.C.
Definition at line 65 of file HomePatch.C.
Definition at line 66 of file HomePatch.C.
int average | ( | CompAtom * | qtilde, |
const HGArrayVector & | q, | ||
BigReal * | lambda, | ||
const int | n, | ||
const int | m, | ||
const HGArrayBigReal & | imass, | ||
const HGArrayBigReal & | length2, | ||
const HGArrayInt & | ial, | ||
const HGArrayInt & | ibl, | ||
const HGArrayVector & | refab, | ||
const BigReal | tolf, | ||
const int | ntrial | ||
) |
Definition at line 4493 of file HomePatch.C.
References endi(), G_q(), iINFO(), iout, lubksb(), ludcmp(), and CompAtom::position.
Referenced by HomePatch::mollyAverage().
Definition at line 456 of file HomePatch.C.
Referenced by HomePatch::buildSpanningTree().
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inline |
Definition at line 4481 of file HomePatch.C.
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inline |
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inline |
Definition at line 4431 of file HomePatch.C.
References NAMD_die(), and TINY.
Referenced by average(), and mollify().
void mollify | ( | CompAtom * | qtilde, |
const HGArrayVector & | q0, | ||
const BigReal * | lambda, | ||
HGArrayVector & | force, | ||
const int | n, | ||
const int | m, | ||
const HGArrayBigReal & | imass, | ||
const HGArrayInt & | ial, | ||
const HGArrayInt & | ibl, | ||
const HGArrayVector & | refab | ||
) |
Definition at line 4675 of file HomePatch.C.
References G_q(), lubksb(), ludcmp(), CompAtom::position, and y.
Referenced by HomePatch::mollyMollify().