org.jmol.minimize.forcefield
Class Calculations
java.lang.Object
org.jmol.minimize.forcefield.Calculations
- Direct Known Subclasses:
- CalculationsUFF
abstract class Calculations
- extends java.lang.Object
Constructor Summary |
Calculations(ForceField ff,
MinAtom[] minAtoms,
MinBond[] minBonds,
int[][] angles,
int[][] torsions,
double[] partialCharges,
java.util.List<java.lang.Object[]> constraints)
|
Method Summary |
(package private) void |
addForce(javax.vecmath.Vector3d v,
int i,
double dE)
|
(package private) void |
appendLogData(java.lang.String s)
|
private double |
calc(int iType,
boolean gradients)
|
(package private) abstract double |
compute(int iType,
java.lang.Object[] dataIn)
|
private double |
constrainQuadratic(double value,
double targetValue,
double k,
int iType)
|
private double |
constraintEnergy(int iType)
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(package private) double |
energyAngle(boolean gradients)
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(package private) double |
energyBond(boolean gradients)
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(package private) double |
energyES(boolean gradients)
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(package private) double |
energyOOP(boolean gradients)
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(package private) double |
energyStrBnd(boolean gradients)
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(package private) double |
energyTorsion(boolean gradients)
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(package private) double |
energyVDW(boolean gradients)
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(package private) abstract java.lang.String |
getAtomList(java.lang.String title)
|
(package private) abstract java.lang.String |
getDebugFooter(int iType,
double energy)
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(package private) abstract java.lang.String |
getDebugHeader(int iType)
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java.lang.String |
getLogData()
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(package private) static FFParam |
getParameter(java.lang.String a,
java.util.Map<java.lang.String,FFParam> ffParams)
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(package private) abstract java.lang.String |
getUnit()
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(package private) boolean |
haveParams()
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void |
setConstraints(java.util.List<java.lang.Object[]> constraints)
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(package private) void |
setLoggingEnabled(boolean TF)
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(package private) void |
setParams(java.util.Map<java.lang.String,FFParam> temp)
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(package private) void |
setPreliminary(boolean TF)
|
void |
setSilent(boolean TF)
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(package private) abstract boolean |
setupCalculations()
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(package private) abstract boolean |
setupElectrostatics()
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Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
RAD_TO_DEG
public static final double RAD_TO_DEG
- See Also:
- Constant Field Values
DEG_TO_RAD
public static final double DEG_TO_RAD
- See Also:
- Constant Field Values
KCAL_TO_KJ
static final double KCAL_TO_KJ
- See Also:
- Constant Field Values
CALC_DISTANCE
static final int CALC_DISTANCE
- See Also:
- Constant Field Values
CALC_ANGLE
static final int CALC_ANGLE
- See Also:
- Constant Field Values
CALC_TORSION
static final int CALC_TORSION
- See Also:
- Constant Field Values
CALC_OOP
static final int CALC_OOP
- See Also:
- Constant Field Values
CALC_VDW
static final int CALC_VDW
- See Also:
- Constant Field Values
CALC_ES
static final int CALC_ES
- See Also:
- Constant Field Values
CALC_MAX
static final int CALC_MAX
- See Also:
- Constant Field Values
ff
ForceField ff
calculations
java.util.List<java.lang.Object[]>[] calculations
ffParams
public java.util.Map<java.lang.String,FFParam> ffParams
atomCount
int atomCount
bondCount
int bondCount
atoms
MinAtom[] atoms
bonds
MinBond[] bonds
angles
int[][] angles
torsions
int[][] torsions
partialCharges
double[] partialCharges
havePartialCharges
boolean havePartialCharges
constraints
java.util.List<java.lang.Object[]> constraints
isPreliminary
boolean isPreliminary
gradients
boolean gradients
silent
boolean silent
logData
java.lang.StringBuffer logData
logging
boolean logging
loggingEnabled
boolean loggingEnabled
da
final javax.vecmath.Vector3d da
db
final javax.vecmath.Vector3d db
dc
final javax.vecmath.Vector3d dc
dd
final javax.vecmath.Vector3d dd
ia
int ia
ib
int ib
ic
int ic
id
int id
v1
final javax.vecmath.Vector3d v1
v2
final javax.vecmath.Vector3d v2
v3
final javax.vecmath.Vector3d v3
PI_OVER_2
private static final double PI_OVER_2
- See Also:
- Constant Field Values
TWO_PI
private static final double TWO_PI
- See Also:
- Constant Field Values
Calculations
Calculations(ForceField ff,
MinAtom[] minAtoms,
MinBond[] minBonds,
int[][] angles,
int[][] torsions,
double[] partialCharges,
java.util.List<java.lang.Object[]> constraints)
setConstraints
public void setConstraints(java.util.List<java.lang.Object[]> constraints)
haveParams
boolean haveParams()
setParams
void setParams(java.util.Map<java.lang.String,FFParam> temp)
getParameter
static FFParam getParameter(java.lang.String a,
java.util.Map<java.lang.String,FFParam> ffParams)
setupCalculations
abstract boolean setupCalculations()
getAtomList
abstract java.lang.String getAtomList(java.lang.String title)
setupElectrostatics
abstract boolean setupElectrostatics()
getDebugHeader
abstract java.lang.String getDebugHeader(int iType)
getDebugFooter
abstract java.lang.String getDebugFooter(int iType,
double energy)
getUnit
abstract java.lang.String getUnit()
compute
abstract double compute(int iType,
java.lang.Object[] dataIn)
addForce
void addForce(javax.vecmath.Vector3d v,
int i,
double dE)
setSilent
public void setSilent(boolean TF)
getLogData
public java.lang.String getLogData()
appendLogData
void appendLogData(java.lang.String s)
setLoggingEnabled
void setLoggingEnabled(boolean TF)
setPreliminary
void setPreliminary(boolean TF)
calc
private double calc(int iType,
boolean gradients)
energyStrBnd
double energyStrBnd(boolean gradients)
energyBond
double energyBond(boolean gradients)
energyAngle
double energyAngle(boolean gradients)
energyTorsion
double energyTorsion(boolean gradients)
energyOOP
double energyOOP(boolean gradients)
energyVDW
double energyVDW(boolean gradients)
energyES
double energyES(boolean gradients)
constraintEnergy
private double constraintEnergy(int iType)
constrainQuadratic
private double constrainQuadratic(double value,
double targetValue,
double k,
int iType)