abstract class Calculations
extends java.lang.Object
Modifier and Type | Field and Description |
---|---|
(package private) int |
ac |
(package private) int |
angleCount |
(package private) int |
bondCount |
(package private) static int |
CALC_ANGLE |
(package private) static int |
CALC_DISTANCE |
(package private) static int |
CALC_ES |
(package private) static int |
CALC_MAX |
(package private) static int |
CALC_OOP |
(package private) static int |
CALC_STRETCH_BEND |
(package private) static int |
CALC_TORSION |
(package private) static int |
CALC_VDW |
(package private) javajs.util.Lst<java.lang.Object[]>[] |
calculations |
(package private) javajs.util.Lst<java.lang.Object[]> |
constraints |
(package private) javajs.util.V3d |
da |
(package private) javajs.util.V3d |
db |
(package private) javajs.util.V3d |
dc |
(package private) javajs.util.V3d |
dd |
static double |
DEG_TO_RAD |
(package private) ForceField |
ff |
(package private) java.util.Map<java.lang.Object,java.lang.Object> |
ffParams |
(package private) boolean |
gradients |
(package private) int |
ia |
(package private) int |
ib |
(package private) int |
ic |
(package private) int |
id |
(package private) boolean |
isPreliminary |
(package private) static double |
KCAL_TO_KJ |
(package private) javajs.util.SB |
logData |
(package private) boolean |
logging |
(package private) boolean |
loggingEnabled |
(package private) MinAngle[] |
minAngles |
(package private) MinAtom[] |
minAtoms |
(package private) MinBond[] |
minBonds |
(package private) MinPosition[] |
minPositions |
(package private) MinTorsion[] |
minTorsions |
(package private) FFParam |
parA |
(package private) FFParam |
parB |
(package private) FFParam |
parC |
private static double |
PI_OVER_2 |
static double |
RAD_TO_DEG |
(package private) boolean |
silent |
(package private) int |
torsionCount |
private static double |
TWO_PI |
(package private) javajs.util.V3d |
v1 |
(package private) javajs.util.V3d |
v2 |
(package private) javajs.util.V3d |
v3 |
Constructor and Description |
---|
Calculations(ForceField ff,
MinAtom[] minAtoms,
MinBond[] minBonds,
MinAngle[] minAngles,
MinTorsion[] minTorsions,
MinPosition[] minPositions,
javajs.util.Lst<java.lang.Object[]> constraints) |
Modifier and Type | Method and Description |
---|---|
(package private) void |
addForce(javajs.util.V3d v,
int i,
double dE) |
(package private) void |
addForces(Calculation c,
int n) |
(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) |
(package private) double |
energyAngle(boolean gradients) |
(package private) double |
energyBond(boolean gradients) |
(package private) double |
energyES(boolean gradients) |
(package private) double |
energyOOP(boolean gradients) |
(package private) double |
energyStrBnd(boolean gradients) |
(package private) double |
energyStretchBend(boolean gradients) |
(package private) double |
energyTorsion(boolean gradients) |
(package private) double |
energyVDW(boolean gradients) |
(package private) java.lang.String |
getAtomList(java.lang.String title) |
(package private) void |
getConstraintList() |
(package private) java.lang.String |
getDebugFooter(int iType,
double energy) |
(package private) abstract java.lang.String |
getDebugHeader(int iType) |
protected java.lang.String |
getDebugHeader2(int iType) |
(package private) java.lang.String |
getDebugLine(int iType,
Calculation c) |
protected java.lang.String |
getDebugLineC(int iType,
Calculation c) |
java.lang.String |
getLogData() |
(package private) java.lang.Object |
getParameter(java.lang.Object o) |
(package private) abstract java.lang.Object |
getParameterObj(MinObject o) |
(package private) abstract java.lang.String |
getUnits() |
(package private) boolean |
isLinear(int i) |
protected void |
pairSearch(javajs.util.Lst<java.lang.Object[]> calc1,
Calculation pc1,
javajs.util.Lst<java.lang.Object[]> calc2,
Calculation pc2) |
(package private) void |
setAngleVariables(Calculation c) |
void |
setConstraints(javajs.util.Lst<java.lang.Object[]> constraints) |
(package private) void |
setCoords(Calculation c,
int n) |
(package private) void |
setLoggingEnabled(boolean TF) |
(package private) void |
setOopVariables(Calculation c,
boolean fixTheta) |
(package private) void |
setPairVariables(Calculation c) |
(package private) void |
setPreliminary(boolean TF) |
void |
setSilent(boolean TF) |
(package private) void |
setTorsionVariables(Calculation c) |
(package private) abstract boolean |
setupCalculations() |
public static final double RAD_TO_DEG
public static final double DEG_TO_RAD
static final double KCAL_TO_KJ
static final int CALC_DISTANCE
static final int CALC_ANGLE
static final int CALC_STRETCH_BEND
static final int CALC_TORSION
static final int CALC_OOP
static final int CALC_VDW
static final int CALC_ES
static final int CALC_MAX
FFParam parA
FFParam parB
FFParam parC
ForceField ff
javajs.util.Lst<java.lang.Object[]>[] calculations
java.util.Map<java.lang.Object,java.lang.Object> ffParams
int ac
int bondCount
int angleCount
int torsionCount
MinAtom[] minAtoms
MinBond[] minBonds
MinAngle[] minAngles
MinTorsion[] minTorsions
MinPosition[] minPositions
javajs.util.Lst<java.lang.Object[]> constraints
boolean isPreliminary
boolean gradients
boolean silent
javajs.util.SB logData
boolean logging
boolean loggingEnabled
final javajs.util.V3d da
final javajs.util.V3d db
final javajs.util.V3d dc
final javajs.util.V3d dd
int ia
int ib
int ic
int id
final javajs.util.V3d v1
final javajs.util.V3d v2
final javajs.util.V3d v3
private static final double PI_OVER_2
private static final double TWO_PI
Calculations(ForceField ff, MinAtom[] minAtoms, MinBond[] minBonds, MinAngle[] minAngles, MinTorsion[] minTorsions, MinPosition[] minPositions, javajs.util.Lst<java.lang.Object[]> constraints)
abstract java.lang.Object getParameterObj(MinObject o)
java.lang.Object getParameter(java.lang.Object o)
public void setConstraints(javajs.util.Lst<java.lang.Object[]> constraints)
abstract boolean setupCalculations()
abstract java.lang.String getUnits()
abstract double compute(int iType, java.lang.Object[] dataIn)
void addForce(javajs.util.V3d v, int i, double dE)
public void setSilent(boolean TF)
public java.lang.String getLogData()
void appendLogData(java.lang.String s)
void setLoggingEnabled(boolean TF)
void setPreliminary(boolean TF)
protected void pairSearch(javajs.util.Lst<java.lang.Object[]> calc1, Calculation pc1, javajs.util.Lst<java.lang.Object[]> calc2, Calculation pc2)
private double calc(int iType, boolean gradients)
double energyStrBnd(boolean gradients)
double energyBond(boolean gradients)
double energyAngle(boolean gradients)
double energyTorsion(boolean gradients)
double energyStretchBend(boolean gradients)
double energyOOP(boolean gradients)
double energyVDW(boolean gradients)
double energyES(boolean gradients)
private double constraintEnergy(int iType)
private double constrainQuadratic(double value, double targetValue, double k, int iType)
void getConstraintList()
java.lang.String getAtomList(java.lang.String title)
abstract java.lang.String getDebugHeader(int iType)
protected java.lang.String getDebugHeader2(int iType)
java.lang.String getDebugLine(int iType, Calculation c)
protected java.lang.String getDebugLineC(int iType, Calculation c)
java.lang.String getDebugFooter(int iType, double energy)
void setPairVariables(Calculation c)
void setAngleVariables(Calculation c)
void setOopVariables(Calculation c, boolean fixTheta)
void setTorsionVariables(Calculation c)
void setCoords(Calculation c, int n)
void addForces(Calculation c, int n)
boolean isLinear(int i)
i
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