struct OutputQuantities
{
//! Energy of this interaction
- real energy = 0;
+ real energy = 0;
//! Derivative with respect to lambda
- real dvdlambda = 0;
+ real dvdlambda = 0;
//! Shift vectors
- rvec fshift[N_IVEC] = {{0}};
+ rvec fshift[N_IVEC] = { { 0 } };
//! Forces
- rvec4 f[c_numAtoms] = {{0}};
+ rvec4 f[c_numAtoms] = { { 0 } };
};
/*! \brief Utility to check the output from bonded tests
* \param[in] checker Reference checker
* \param[in] output The output from the test to check
*/
-void checkOutput(test::TestReferenceChecker *checker,
- const OutputQuantities &output)
+void checkOutput(test::TestReferenceChecker* checker, const OutputQuantities& output)
{
checker->checkReal(output.energy, "Epot ");
// Should still be zero if not doing FEP, so may as well test it.
*/
struct iListInput
{
- public:
- //! Function type
- int ftype = -1;
- //! Tolerance for float evaluation
- float ftoler = 1e-6;
- //! Tolerance for double evaluation
- double dtoler = 1e-8;
- //! Do free energy perturbation?
- bool fep = false;
- //! Interaction parameters
- t_iparams iparams = {{ 0 }};
-
- //! Constructor
- iListInput() {}
-
- /*! \brief Constructor with tolerance
- *
- * \param[in] ftol Single precision tolerance
- * \param[in] dtol Double precision tolerance
- */
- iListInput(float ftol, double dtol)
- {
- ftoler = ftol;
- dtoler = dtol;
- }
- /*! \brief Set parameters for harmonic potential
- *
- * Free energy perturbation is turned on when A
- * and B parameters are different.
- * \param[in] ft Function type
- * \param[in] rA Equilibrium value A
- * \param[in] krA Force constant A
- * \param[in] rB Equilibrium value B
- * \param[in] krB Force constant B
- * \return The structure itself.
- */
- iListInput setHarmonic(int ft, real rA, real krA, real rB, real krB)
- {
- iparams.harmonic.rA = rA;
- iparams.harmonic.rB = rB;
- iparams.harmonic.krA = krA;
- iparams.harmonic.krB = krB;
- ftype = ft;
- fep = (rA != rB || krA != krB);
- return *this;
- }
- /*! \brief Set parameters for harmonic potential
- *
- * \param[in] ft Function type
- * \param[in] rA Equilibrium value
- * \param[in] krA Force constant
- * \return The structure itself.
- */
- iListInput setHarmonic(int ft, real rA, real krA)
- {
- return setHarmonic(ft, rA, krA, rA, krA);
- }
- /*! \brief Set parameters for cubic potential
- *
- * \param[in] b0 Equilibrium bond length
- * \param[in] kb Harmonic force constant
- * \param[in] kcub Cubic force constant
- * \return The structure itself.
- */
- iListInput setCubic(real b0, real kb, real kcub)
- {
- ftype = F_CUBICBONDS;
- iparams.cubic.b0 = b0;
- iparams.cubic.kb = kb;
- iparams.cubic.kcub = kcub;
- return *this;
- }
- /*! \brief Set parameters for morse potential
- *
- * Free energy perturbation is turned on when A
- * and B parameters are different.
- * \param[in] b0A Equilibrium value A
- * \param[in] cbA Force constant A
- * \param[in] betaA Steepness parameter A
- * \param[in] b0B Equilibrium value B
- * \param[in] cbB Force constant B
- * \param[in] betaB Steepness parameter B
- * \return The structure itself.
- */
- iListInput setMorse(real b0A, real cbA, real betaA, real b0B, real cbB, real betaB)
- {
- ftype = F_MORSE;
- iparams.morse.b0A = b0A;
- iparams.morse.cbA = cbA;
- iparams.morse.betaA = betaA;
- iparams.morse.b0B = b0B;
- iparams.morse.cbB = cbB;
- iparams.morse.betaB = betaB;
- fep = (b0A != b0B || cbA != cbB || betaA != betaB);
- return *this;
- }
- /*! \brief Set parameters for morse potential
- *
- * \param[in] b0A Equilibrium value
- * \param[in] cbA Force constant
- * \param[in] betaA Steepness parameter
- * \return The structure itself.
- */
- iListInput setMorse(real b0A, real cbA, real betaA)
- {
- return setMorse(b0A, cbA, betaA, b0A, cbA, betaA);
- }
- /*! \brief Set parameters for fene potential
- *
- * \param[in] bm Equilibrium bond length
- * \param[in] kb Force constant
- * \return The structure itself.
- */
- iListInput setFene(real bm, real kb)
- {
- ftype = F_FENEBONDS;
- iparams.fene.bm = bm;
- iparams.fene.kb = kb;
- return *this;
- }
- /*! \brief Set parameters for linear angle potential
- *
- * Free energy perturbation is turned on when A
- * and B parameters are different.
- * \param[in] klinA Force constant A
- * \param[in] aA The position of the central atom A
- * \param[in] klinB Force constant B
- * \param[in] aB The position of the central atom B
- * \return The structure itself.
- */
- iListInput setLinearAngle(real klinA, real aA, real klinB, real aB)
- {
- ftype = F_LINEAR_ANGLES;
- iparams.linangle.klinA = klinA;
- iparams.linangle.aA = aA;
- iparams.linangle.klinB = klinB;
- iparams.linangle.aB = aB;
- fep = (klinA != klinB || aA != aB);
- return *this;
- }
- /*! \brief Set parameters for linear angle potential
- *
- * \param[in] klinA Force constant
- * \param[in] aA The position of the central atom
- * \return The structure itself.
- */
- iListInput setLinearAngle(real klinA, real aA)
- {
- return setLinearAngle(klinA, aA, klinA, aA);
- }
- /*! \brief Set parameters for Urey Bradley potential
- *
- * Free energy perturbation is turned on when A
- * and B parameters are different.
- * \param[in] thetaA Equilibrium angle A
- * \param[in] kthetaA Force constant A
- * \param[in] r13A The distance between i and k atoms A
- * \param[in] kUBA The force constant for 1-3 distance A
- * \param[in] thetaB Equilibrium angle B
- * \param[in] kthetaB Force constant B
- * \param[in] r13B The distance between i and k atoms B
- * \param[in] kUBB The force constant for 1-3 distance B
- * \return The structure itself.
- */
- iListInput setUreyBradley(real thetaA, real kthetaA, real r13A, real kUBA,
- real thetaB, real kthetaB, real r13B, real kUBB)
- {
- ftype = F_UREY_BRADLEY;
- iparams.u_b.thetaA = thetaA;
- iparams.u_b.kthetaA = kthetaA;
- iparams.u_b.r13A = r13A;
- iparams.u_b.kUBA = kUBA;
- iparams.u_b.thetaB = thetaB;
- iparams.u_b.kthetaB = kthetaB;
- iparams.u_b.r13B = r13B;
- iparams.u_b.kUBB = kUBB;
- fep = (thetaA != thetaB || kthetaA != kthetaB || r13A != r13B || kUBA != kUBB);
- return *this;
- }
- /*! \brief Set parameters for Urey Bradley potential
- *
- * \param[in] thetaA Equilibrium angle
- * \param[in] kthetaA Force constant
- * \param[in] r13A The distance between i and k atoms
- * \param[in] kUBA The force constant for 1-3 distance
- * \return The structure itself.
- */
- iListInput setUreyBradley(real thetaA, real kthetaA, real r13A, real kUBA)
- {
- return setUreyBradley(thetaA, kthetaA, r13A, kUBA,
- thetaA, kthetaA, r13A, kUBA);
- }
- /*! \brief Set parameters for Cross Bond Bonds potential
- *
- * \param[in] r1e First bond length i-j
- * \param[in] r2e Second bond length i-k
- * \param[in] krr The force constant
- * \return The structure itself.
- */
- iListInput setCrossBondBonds(real r1e, real r2e, real krr)
- {
- ftype = F_CROSS_BOND_BONDS;
- iparams.cross_bb.r1e = r1e;
- iparams.cross_bb.r2e = r2e;
- iparams.cross_bb.krr = krr;
- return *this;
- }
- /*! \brief Set parameters for Cross Bond Angles potential
- *
- * \param[in] r1e First bond length i-j
- * \param[in] r2e Second bond length j-k
- * \param[in] r3e Third bond length i-k
- * \param[in] krt The force constant
- * \return The structure itself.
- */
- iListInput setCrossBondAngles(real r1e, real r2e, real r3e, real krt)
- {
- ftype = F_CROSS_BOND_ANGLES;
- iparams.cross_ba.r1e = r1e;
- iparams.cross_ba.r2e = r2e;
- iparams.cross_ba.r3e = r3e;
- iparams.cross_ba.krt = krt;
- return *this;
- }
- /*! \brief Set parameters for Quartic Angles potential
- *
- * \param[in] theta Angle
- * \param[in] c Array of parameters
- * \return The structure itself.
- */
- iListInput setQuarticAngles(real theta, const real c[5])
- {
- ftype = F_QUARTIC_ANGLES;
- iparams.qangle.theta = theta;
- iparams.qangle.c[0] = c[0];
- iparams.qangle.c[1] = c[1];
- iparams.qangle.c[2] = c[2];
- iparams.qangle.c[3] = c[3];
- iparams.qangle.c[4] = c[4];
- return *this;
- }
- /*! \brief Set parameters for proper dihedrals potential
- *
- * Free energy perturbation is turned on when A
- * and B parameters are different.
- * \param[in] ft Function type
- * \param[in] phiA Dihedral angle A
- * \param[in] cpA Force constant A
- * \param[in] mult Multiplicity of the angle
- * \param[in] phiB Dihedral angle B
- * \param[in] cpB Force constant B
- * \return The structure itself.
- */
- iListInput setPDihedrals(int ft, real phiA, real cpA, int mult, real phiB, real cpB)
- {
- ftype = ft;
- iparams.pdihs.phiA = phiA;
- iparams.pdihs.cpA = cpA;
- iparams.pdihs.phiB = phiB;
- iparams.pdihs.cpB = cpB;
- iparams.pdihs.mult = mult;
- fep = (phiA != phiB || cpA != cpB);
- return *this;
- }
- /*! \brief Set parameters for proper dihedrals potential
- *
- * \param[in] ft Function type
- * \param[in] phiA Dihedral angle
- * \param[in] cpA Force constant
- * \param[in] mult Multiplicity of the angle
- * \return The structure itself.
- */
- iListInput setPDihedrals(int ft, real phiA, real cpA, int mult)
- {
- return setPDihedrals(ft, phiA, cpA, mult, phiA, cpA);
- }
- /*! \brief Set parameters for Ryckaert-Bellemans dihedrals potential
- *
- * Free energy perturbation is turned on when A
- * and B parameters are different.
- * \param[in] rbcA Force constants A
- * \param[in] rbcB Force constants B
- * \return The structure itself.
- */
- iListInput setRbDihedrals(const real rbcA[NR_RBDIHS], const real rbcB[NR_RBDIHS])
- {
- ftype = F_RBDIHS;
- fep = false;
- for (int i = 0; i < NR_RBDIHS; i++)
- {
- iparams.rbdihs.rbcA[i] = rbcA[i];
- iparams.rbdihs.rbcB[i] = rbcB[i];
- fep = fep || (rbcA[i] != rbcB[i]);
- }
- return *this;
- }
- /*! \brief Set parameters for Ryckaert-Bellemans dihedrals potential
- *
- * \param[in] rbc Force constants
- * \return The structure itself.
- */
- iListInput setRbDihedrals(const real rbc[NR_RBDIHS])
- {
- return setRbDihedrals(rbc, rbc);
- }
- /*! \brief Set parameters for Polarization
- *
- * \param[in] alpha Polarizability
- * \return The structure itself.
- */
- iListInput setPolarization(real alpha)
- {
- ftype = F_POLARIZATION;
- fep = false;
- iparams.polarize.alpha = alpha;
- return *this;
- }
- /*! \brief Set parameters for Anharmonic Polarization
- *
- * \param[in] alpha Polarizability (nm^3)
- * \param[in] drcut The cut-off distance (nm) after which the
- * fourth power kicks in
- * \param[in] khyp The force constant for the fourth power
- * \return The structure itself.
- */
- iListInput setAnharmPolarization(real alpha,
- real drcut,
- real khyp)
- {
- ftype = F_ANHARM_POL;
- fep = false;
- iparams.anharm_polarize.alpha = alpha;
- iparams.anharm_polarize.drcut = drcut;
- iparams.anharm_polarize.khyp = khyp;
- return *this;
- }
- /*! \brief Set parameters for Thole Polarization
- *
- * \param[in] a Thole factor
- * \param[in] alpha1 Polarizability 1 (nm^3)
- * \param[in] alpha2 Polarizability 2 (nm^3)
- * \param[in] rfac Distance factor
- * \return The structure itself.
- */
- iListInput setTholePolarization(real a,
- real alpha1,
- real alpha2,
- real rfac)
- {
- ftype = F_THOLE_POL;
- fep = false;
- iparams.thole.a = a;
- iparams.thole.alpha1 = alpha1;
- iparams.thole.alpha2 = alpha2;
- iparams.thole.rfac = rfac;
- return *this;
- }
- /*! \brief Set parameters for Water Polarization
- *
- * \param[in] alpha_x Polarizability X (nm^3)
- * \param[in] alpha_y Polarizability Y (nm^3)
- * \param[in] alpha_z Polarizability Z (nm^3)
- * \param[in] rOH Oxygen-Hydrogen distance
- * \param[in] rHH Hydrogen-Hydrogen distance
- * \param[in] rOD Oxygen-Dummy distance
- * \return The structure itself.
- */
- iListInput setWaterPolarization(real alpha_x,
- real alpha_y,
- real alpha_z,
- real rOH,
- real rHH,
- real rOD)
+public:
+ //! Function type
+ int ftype = -1;
+ //! Tolerance for float evaluation
+ float ftoler = 1e-6;
+ //! Tolerance for double evaluation
+ double dtoler = 1e-8;
+ //! Do free energy perturbation?
+ bool fep = false;
+ //! Interaction parameters
+ t_iparams iparams = { { 0 } };
+
+ //! Constructor
+ iListInput() {}
+
+ /*! \brief Constructor with tolerance
+ *
+ * \param[in] ftol Single precision tolerance
+ * \param[in] dtol Double precision tolerance
+ */
+ iListInput(float ftol, double dtol)
+ {
+ ftoler = ftol;
+ dtoler = dtol;
+ }
+ /*! \brief Set parameters for harmonic potential
+ *
+ * Free energy perturbation is turned on when A
+ * and B parameters are different.
+ * \param[in] ft Function type
+ * \param[in] rA Equilibrium value A
+ * \param[in] krA Force constant A
+ * \param[in] rB Equilibrium value B
+ * \param[in] krB Force constant B
+ * \return The structure itself.
+ */
+ iListInput setHarmonic(int ft, real rA, real krA, real rB, real krB)
+ {
+ iparams.harmonic.rA = rA;
+ iparams.harmonic.rB = rB;
+ iparams.harmonic.krA = krA;
+ iparams.harmonic.krB = krB;
+ ftype = ft;
+ fep = (rA != rB || krA != krB);
+ return *this;
+ }
+ /*! \brief Set parameters for harmonic potential
+ *
+ * \param[in] ft Function type
+ * \param[in] rA Equilibrium value
+ * \param[in] krA Force constant
+ * \return The structure itself.
+ */
+ iListInput setHarmonic(int ft, real rA, real krA) { return setHarmonic(ft, rA, krA, rA, krA); }
+ /*! \brief Set parameters for cubic potential
+ *
+ * \param[in] b0 Equilibrium bond length
+ * \param[in] kb Harmonic force constant
+ * \param[in] kcub Cubic force constant
+ * \return The structure itself.
+ */
+ iListInput setCubic(real b0, real kb, real kcub)
+ {
+ ftype = F_CUBICBONDS;
+ iparams.cubic.b0 = b0;
+ iparams.cubic.kb = kb;
+ iparams.cubic.kcub = kcub;
+ return *this;
+ }
+ /*! \brief Set parameters for morse potential
+ *
+ * Free energy perturbation is turned on when A
+ * and B parameters are different.
+ * \param[in] b0A Equilibrium value A
+ * \param[in] cbA Force constant A
+ * \param[in] betaA Steepness parameter A
+ * \param[in] b0B Equilibrium value B
+ * \param[in] cbB Force constant B
+ * \param[in] betaB Steepness parameter B
+ * \return The structure itself.
+ */
+ iListInput setMorse(real b0A, real cbA, real betaA, real b0B, real cbB, real betaB)
+ {
+ ftype = F_MORSE;
+ iparams.morse.b0A = b0A;
+ iparams.morse.cbA = cbA;
+ iparams.morse.betaA = betaA;
+ iparams.morse.b0B = b0B;
+ iparams.morse.cbB = cbB;
+ iparams.morse.betaB = betaB;
+ fep = (b0A != b0B || cbA != cbB || betaA != betaB);
+ return *this;
+ }
+ /*! \brief Set parameters for morse potential
+ *
+ * \param[in] b0A Equilibrium value
+ * \param[in] cbA Force constant
+ * \param[in] betaA Steepness parameter
+ * \return The structure itself.
+ */
+ iListInput setMorse(real b0A, real cbA, real betaA)
+ {
+ return setMorse(b0A, cbA, betaA, b0A, cbA, betaA);
+ }
+ /*! \brief Set parameters for fene potential
+ *
+ * \param[in] bm Equilibrium bond length
+ * \param[in] kb Force constant
+ * \return The structure itself.
+ */
+ iListInput setFene(real bm, real kb)
+ {
+ ftype = F_FENEBONDS;
+ iparams.fene.bm = bm;
+ iparams.fene.kb = kb;
+ return *this;
+ }
+ /*! \brief Set parameters for linear angle potential
+ *
+ * Free energy perturbation is turned on when A
+ * and B parameters are different.
+ * \param[in] klinA Force constant A
+ * \param[in] aA The position of the central atom A
+ * \param[in] klinB Force constant B
+ * \param[in] aB The position of the central atom B
+ * \return The structure itself.
+ */
+ iListInput setLinearAngle(real klinA, real aA, real klinB, real aB)
+ {
+ ftype = F_LINEAR_ANGLES;
+ iparams.linangle.klinA = klinA;
+ iparams.linangle.aA = aA;
+ iparams.linangle.klinB = klinB;
+ iparams.linangle.aB = aB;
+ fep = (klinA != klinB || aA != aB);
+ return *this;
+ }
+ /*! \brief Set parameters for linear angle potential
+ *
+ * \param[in] klinA Force constant
+ * \param[in] aA The position of the central atom
+ * \return The structure itself.
+ */
+ iListInput setLinearAngle(real klinA, real aA) { return setLinearAngle(klinA, aA, klinA, aA); }
+ /*! \brief Set parameters for Urey Bradley potential
+ *
+ * Free energy perturbation is turned on when A
+ * and B parameters are different.
+ * \param[in] thetaA Equilibrium angle A
+ * \param[in] kthetaA Force constant A
+ * \param[in] r13A The distance between i and k atoms A
+ * \param[in] kUBA The force constant for 1-3 distance A
+ * \param[in] thetaB Equilibrium angle B
+ * \param[in] kthetaB Force constant B
+ * \param[in] r13B The distance between i and k atoms B
+ * \param[in] kUBB The force constant for 1-3 distance B
+ * \return The structure itself.
+ */
+ iListInput
+ setUreyBradley(real thetaA, real kthetaA, real r13A, real kUBA, real thetaB, real kthetaB, real r13B, real kUBB)
+ {
+ ftype = F_UREY_BRADLEY;
+ iparams.u_b.thetaA = thetaA;
+ iparams.u_b.kthetaA = kthetaA;
+ iparams.u_b.r13A = r13A;
+ iparams.u_b.kUBA = kUBA;
+ iparams.u_b.thetaB = thetaB;
+ iparams.u_b.kthetaB = kthetaB;
+ iparams.u_b.r13B = r13B;
+ iparams.u_b.kUBB = kUBB;
+ fep = (thetaA != thetaB || kthetaA != kthetaB || r13A != r13B || kUBA != kUBB);
+ return *this;
+ }
+ /*! \brief Set parameters for Urey Bradley potential
+ *
+ * \param[in] thetaA Equilibrium angle
+ * \param[in] kthetaA Force constant
+ * \param[in] r13A The distance between i and k atoms
+ * \param[in] kUBA The force constant for 1-3 distance
+ * \return The structure itself.
+ */
+ iListInput setUreyBradley(real thetaA, real kthetaA, real r13A, real kUBA)
+ {
+ return setUreyBradley(thetaA, kthetaA, r13A, kUBA, thetaA, kthetaA, r13A, kUBA);
+ }
+ /*! \brief Set parameters for Cross Bond Bonds potential
+ *
+ * \param[in] r1e First bond length i-j
+ * \param[in] r2e Second bond length i-k
+ * \param[in] krr The force constant
+ * \return The structure itself.
+ */
+ iListInput setCrossBondBonds(real r1e, real r2e, real krr)
+ {
+ ftype = F_CROSS_BOND_BONDS;
+ iparams.cross_bb.r1e = r1e;
+ iparams.cross_bb.r2e = r2e;
+ iparams.cross_bb.krr = krr;
+ return *this;
+ }
+ /*! \brief Set parameters for Cross Bond Angles potential
+ *
+ * \param[in] r1e First bond length i-j
+ * \param[in] r2e Second bond length j-k
+ * \param[in] r3e Third bond length i-k
+ * \param[in] krt The force constant
+ * \return The structure itself.
+ */
+ iListInput setCrossBondAngles(real r1e, real r2e, real r3e, real krt)
+ {
+ ftype = F_CROSS_BOND_ANGLES;
+ iparams.cross_ba.r1e = r1e;
+ iparams.cross_ba.r2e = r2e;
+ iparams.cross_ba.r3e = r3e;
+ iparams.cross_ba.krt = krt;
+ return *this;
+ }
+ /*! \brief Set parameters for Quartic Angles potential
+ *
+ * \param[in] theta Angle
+ * \param[in] c Array of parameters
+ * \return The structure itself.
+ */
+ iListInput setQuarticAngles(real theta, const real c[5])
+ {
+ ftype = F_QUARTIC_ANGLES;
+ iparams.qangle.theta = theta;
+ iparams.qangle.c[0] = c[0];
+ iparams.qangle.c[1] = c[1];
+ iparams.qangle.c[2] = c[2];
+ iparams.qangle.c[3] = c[3];
+ iparams.qangle.c[4] = c[4];
+ return *this;
+ }
+ /*! \brief Set parameters for proper dihedrals potential
+ *
+ * Free energy perturbation is turned on when A
+ * and B parameters are different.
+ * \param[in] ft Function type
+ * \param[in] phiA Dihedral angle A
+ * \param[in] cpA Force constant A
+ * \param[in] mult Multiplicity of the angle
+ * \param[in] phiB Dihedral angle B
+ * \param[in] cpB Force constant B
+ * \return The structure itself.
+ */
+ iListInput setPDihedrals(int ft, real phiA, real cpA, int mult, real phiB, real cpB)
+ {
+ ftype = ft;
+ iparams.pdihs.phiA = phiA;
+ iparams.pdihs.cpA = cpA;
+ iparams.pdihs.phiB = phiB;
+ iparams.pdihs.cpB = cpB;
+ iparams.pdihs.mult = mult;
+ fep = (phiA != phiB || cpA != cpB);
+ return *this;
+ }
+ /*! \brief Set parameters for proper dihedrals potential
+ *
+ * \param[in] ft Function type
+ * \param[in] phiA Dihedral angle
+ * \param[in] cpA Force constant
+ * \param[in] mult Multiplicity of the angle
+ * \return The structure itself.
+ */
+ iListInput setPDihedrals(int ft, real phiA, real cpA, int mult)
+ {
+ return setPDihedrals(ft, phiA, cpA, mult, phiA, cpA);
+ }
+ /*! \brief Set parameters for Ryckaert-Bellemans dihedrals potential
+ *
+ * Free energy perturbation is turned on when A
+ * and B parameters are different.
+ * \param[in] rbcA Force constants A
+ * \param[in] rbcB Force constants B
+ * \return The structure itself.
+ */
+ iListInput setRbDihedrals(const real rbcA[NR_RBDIHS], const real rbcB[NR_RBDIHS])
+ {
+ ftype = F_RBDIHS;
+ fep = false;
+ for (int i = 0; i < NR_RBDIHS; i++)
{
- ftype = F_WATER_POL;
- fep = false;
- iparams.wpol.al_x = alpha_x;
- iparams.wpol.al_y = alpha_y;
- iparams.wpol.al_z = alpha_z;
- iparams.wpol.rOH = rOH;
- iparams.wpol.rHH = rHH;
- iparams.wpol.rOD = rOD;
- return *this;
+ iparams.rbdihs.rbcA[i] = rbcA[i];
+ iparams.rbdihs.rbcB[i] = rbcB[i];
+ fep = fep || (rbcA[i] != rbcB[i]);
}
+ return *this;
+ }
+ /*! \brief Set parameters for Ryckaert-Bellemans dihedrals potential
+ *
+ * \param[in] rbc Force constants
+ * \return The structure itself.
+ */
+ iListInput setRbDihedrals(const real rbc[NR_RBDIHS]) { return setRbDihedrals(rbc, rbc); }
+ /*! \brief Set parameters for Polarization
+ *
+ * \param[in] alpha Polarizability
+ * \return The structure itself.
+ */
+ iListInput setPolarization(real alpha)
+ {
+ ftype = F_POLARIZATION;
+ fep = false;
+ iparams.polarize.alpha = alpha;
+ return *this;
+ }
+ /*! \brief Set parameters for Anharmonic Polarization
+ *
+ * \param[in] alpha Polarizability (nm^3)
+ * \param[in] drcut The cut-off distance (nm) after which the
+ * fourth power kicks in
+ * \param[in] khyp The force constant for the fourth power
+ * \return The structure itself.
+ */
+ iListInput setAnharmPolarization(real alpha, real drcut, real khyp)
+ {
+ ftype = F_ANHARM_POL;
+ fep = false;
+ iparams.anharm_polarize.alpha = alpha;
+ iparams.anharm_polarize.drcut = drcut;
+ iparams.anharm_polarize.khyp = khyp;
+ return *this;
+ }
+ /*! \brief Set parameters for Thole Polarization
+ *
+ * \param[in] a Thole factor
+ * \param[in] alpha1 Polarizability 1 (nm^3)
+ * \param[in] alpha2 Polarizability 2 (nm^3)
+ * \param[in] rfac Distance factor
+ * \return The structure itself.
+ */
+ iListInput setTholePolarization(real a, real alpha1, real alpha2, real rfac)
+ {
+ ftype = F_THOLE_POL;
+ fep = false;
+ iparams.thole.a = a;
+ iparams.thole.alpha1 = alpha1;
+ iparams.thole.alpha2 = alpha2;
+ iparams.thole.rfac = rfac;
+ return *this;
+ }
+ /*! \brief Set parameters for Water Polarization
+ *
+ * \param[in] alpha_x Polarizability X (nm^3)
+ * \param[in] alpha_y Polarizability Y (nm^3)
+ * \param[in] alpha_z Polarizability Z (nm^3)
+ * \param[in] rOH Oxygen-Hydrogen distance
+ * \param[in] rHH Hydrogen-Hydrogen distance
+ * \param[in] rOD Oxygen-Dummy distance
+ * \return The structure itself.
+ */
+ iListInput setWaterPolarization(real alpha_x, real alpha_y, real alpha_z, real rOH, real rHH, real rOD)
+ {
+ ftype = F_WATER_POL;
+ fep = false;
+ iparams.wpol.al_x = alpha_x;
+ iparams.wpol.al_y = alpha_y;
+ iparams.wpol.al_z = alpha_z;
+ iparams.wpol.rOH = rOH;
+ iparams.wpol.rHH = rHH;
+ iparams.wpol.rOD = rOD;
+ return *this;
+ }
};
/*! \brief Utility to fill iatoms struct
* \param[in] ftype Function type
* \param[out] iatoms Pointer to iatoms struct
*/
-void fillIatoms(int ftype, std::vector<t_iatom> *iatoms)
+void fillIatoms(int ftype, std::vector<t_iatom>* iatoms)
{
- std::unordered_map<int, std::vector<int> > ia =
- { { 2, { 0, 0, 1, 0, 1, 2, 0, 2, 3 } },
- { 3, { 0, 0, 1, 2, 0, 1, 2, 3 } },
- { 4, { 0, 0, 1, 2, 3 } },
- { 5, { 0, 0, 1, 2, 3, 0 } } };
+ std::unordered_map<int, std::vector<int>> ia = { { 2, { 0, 0, 1, 0, 1, 2, 0, 2, 3 } },
+ { 3, { 0, 0, 1, 2, 0, 1, 2, 3 } },
+ { 4, { 0, 0, 1, 2, 3 } },
+ { 5, { 0, 0, 1, 2, 3, 0 } } };
EXPECT_TRUE(ftype >= 0 && ftype < F_NRE);
int nral = interaction_function[ftype].nratoms;
- for (auto &i : ia[nral])
+ for (auto& i : ia[nral])
{
iatoms->push_back(i);
}
}
-class ListedForcesTest : public ::testing::TestWithParam<std::tuple<iListInput, std::vector<gmx::RVec>, int> >
+class ListedForcesTest :
+ public ::testing::TestWithParam<std::tuple<iListInput, std::vector<gmx::RVec>, int>>
{
- protected:
- matrix box_;
- t_pbc pbc_;
- std::vector<gmx::RVec> x_;
- int epbc_;
- iListInput input_;
- test::TestReferenceData refData_;
- test::TestReferenceChecker checker_;
- ListedForcesTest( ) :
- checker_(refData_.rootChecker())
- {
- input_ = std::get<0>(GetParam());
- x_ = std::get<1>(GetParam());
- epbc_ = std::get<2>(GetParam());
- clear_mat(box_);
- box_[0][0] = box_[1][1] = box_[2][2] = 1.5;
- set_pbc(&pbc_, epbc_, box_);
- // We need quite specific tolerances here since angle functions
- // etc. are not very precise and reproducible.
- test::FloatingPointTolerance tolerance(test::FloatingPointTolerance(input_.ftoler, 1.0e-6,
- input_.dtoler, 1.0e-12,
- 10000, 100, false));
- checker_.setDefaultTolerance(tolerance);
- }
- void testOneIfunc(test::TestReferenceChecker *checker,
- const std::vector<t_iatom> &iatoms,
- const real lambda)
- {
- SCOPED_TRACE(std::string("Testing PBC ") + epbc_names[epbc_]);
- std::vector<int> ddgatindex = { 0, 1, 2, 3 };
- std::vector<real> chargeA = { 1.5, -2.0, 1.5, -1.0 };
- t_mdatoms mdatoms = {0};
- mdatoms.chargeA = chargeA.data();
- OutputQuantities output;
- output.energy = calculateSimpleBond(input_.ftype,
- iatoms.size(),
- iatoms.data(),
- &input_.iparams,
- as_rvec_array(x_.data()),
- output.f, output.fshift,
- &pbc_,
- /* const struct t_graph *g */ nullptr,
- lambda, &output.dvdlambda,
- &mdatoms,
- /* struct t_fcdata * */ nullptr,
- ddgatindex.data(),
- BondedKernelFlavor::ForcesAndVirialAndEnergy);
- // Internal consistency test of both test input
- // and bonded functions.
- EXPECT_TRUE((input_.fep || (output.dvdlambda == 0.0)));
- checkOutput(checker, output);
- }
- void testIfunc()
+protected:
+ matrix box_;
+ t_pbc pbc_;
+ std::vector<gmx::RVec> x_;
+ int epbc_;
+ iListInput input_;
+ test::TestReferenceData refData_;
+ test::TestReferenceChecker checker_;
+ ListedForcesTest() : checker_(refData_.rootChecker())
+ {
+ input_ = std::get<0>(GetParam());
+ x_ = std::get<1>(GetParam());
+ epbc_ = std::get<2>(GetParam());
+ clear_mat(box_);
+ box_[0][0] = box_[1][1] = box_[2][2] = 1.5;
+ set_pbc(&pbc_, epbc_, box_);
+ // We need quite specific tolerances here since angle functions
+ // etc. are not very precise and reproducible.
+ test::FloatingPointTolerance tolerance(test::FloatingPointTolerance(
+ input_.ftoler, 1.0e-6, input_.dtoler, 1.0e-12, 10000, 100, false));
+ checker_.setDefaultTolerance(tolerance);
+ }
+ void testOneIfunc(test::TestReferenceChecker* checker, const std::vector<t_iatom>& iatoms, const real lambda)
+ {
+ SCOPED_TRACE(std::string("Testing PBC ") + epbc_names[epbc_]);
+ std::vector<int> ddgatindex = { 0, 1, 2, 3 };
+ std::vector<real> chargeA = { 1.5, -2.0, 1.5, -1.0 };
+ t_mdatoms mdatoms = { 0 };
+ mdatoms.chargeA = chargeA.data();
+ OutputQuantities output;
+ output.energy = calculateSimpleBond(
+ input_.ftype, iatoms.size(), iatoms.data(), &input_.iparams,
+ as_rvec_array(x_.data()), output.f, output.fshift, &pbc_,
+ /* const struct t_graph *g */ nullptr, lambda, &output.dvdlambda, &mdatoms,
+ /* struct t_fcdata * */ nullptr, ddgatindex.data(),
+ BondedKernelFlavor::ForcesAndVirialAndEnergy);
+ // Internal consistency test of both test input
+ // and bonded functions.
+ EXPECT_TRUE((input_.fep || (output.dvdlambda == 0.0)));
+ checkOutput(checker, output);
+ }
+ void testIfunc()
+ {
+ test::TestReferenceChecker thisChecker =
+ checker_.checkCompound("FunctionType", interaction_function[input_.ftype].name)
+ .checkCompound("FEP", (input_.fep ? "Yes" : "No"));
+ std::vector<t_iatom> iatoms;
+ fillIatoms(input_.ftype, &iatoms);
+ if (input_.fep)
{
- test::TestReferenceChecker thisChecker =
- checker_.checkCompound("FunctionType",
- interaction_function[input_.ftype].name).checkCompound("FEP", (input_.fep ? "Yes" : "No"));
- std::vector<t_iatom> iatoms;
- fillIatoms(input_.ftype, &iatoms);
- if (input_.fep)
- {
- const int numLambdas = 3;
- for (int i = 0; i < numLambdas; ++i)
- {
- const real lambda = i / (numLambdas - 1.0);
- auto valueChecker = thisChecker.checkCompound("Lambda", toString(lambda));
- testOneIfunc(&valueChecker, iatoms, lambda);
- }
- }
- else
+ const int numLambdas = 3;
+ for (int i = 0; i < numLambdas; ++i)
{
- testOneIfunc(&thisChecker, iatoms, 0.0);
+ const real lambda = i / (numLambdas - 1.0);
+ auto valueChecker = thisChecker.checkCompound("Lambda", toString(lambda));
+ testOneIfunc(&valueChecker, iatoms, lambda);
}
}
+ else
+ {
+ testOneIfunc(&thisChecker, iatoms, 0.0);
+ }
+ }
};
-TEST_P (ListedForcesTest, Ifunc)
+TEST_P(ListedForcesTest, Ifunc)
{
testIfunc();
}
//! Function types for testing bonds. Add new terms at the end.
-std::vector<iListInput> c_InputBonds =
-{
+std::vector<iListInput> c_InputBonds = {
{ iListInput().setHarmonic(F_BONDS, 0.15, 500.0) },
{ iListInput(2e-6F, 1e-8).setHarmonic(F_BONDS, 0.15, 500.0, 0.17, 400.0) },
{ iListInput(1e-4F, 1e-8).setHarmonic(F_G96BONDS, 0.15, 50.0) },
const real cQuarticAngles[5] = { 1.1, 2.3, 4.6, 7.8, 9.2 };
//! Function types for testing angles. Add new terms at the end.
-std::vector<iListInput> c_InputAngles =
-{
+std::vector<iListInput> c_InputAngles = {
{ iListInput(2e-3, 1e-8).setHarmonic(F_ANGLES, 100.0, 50.0) },
{ iListInput(2e-3, 1e-8).setHarmonic(F_ANGLES, 100.15, 50.0, 95.0, 30.0) },
{ iListInput(8e-3, 1e-8).setHarmonic(F_G96ANGLES, 100.0, 50.0) },
{ iListInput(2e-6, 1e-8).setCrossBondAngles(0.8, 0.7, 0.3, 45.0) },
{ iListInput(2e-2, 1e-8).setUreyBradley(950.0, 46.0, 0.3, 5.0) },
{ iListInput(2e-2, 1e-8).setUreyBradley(100.0, 45.0, 0.3, 5.0, 90.0, 47.0, 0.32, 7.0) },
- { iListInput(2e-3, 1e-8).setQuarticAngles(87.0, cQuarticAngles ) }
+ { iListInput(2e-3, 1e-8).setQuarticAngles(87.0, cQuarticAngles) }
};
//! Constants for Ryckaert-Bellemans A
const real rbc[NR_RBDIHS] = { -7.35, 13.6, 8.4, -16.7, 1.3, 12.4 };
//! Function types for testing dihedrals. Add new terms at the end.
-std::vector<iListInput> c_InputDihs =
-{
+std::vector<iListInput> c_InputDihs = {
{ iListInput(1e-4, 1e-8).setPDihedrals(F_PDIHS, -100.0, 10.0, 2, -80.0, 20.0) },
{ iListInput(1e-4, 1e-8).setPDihedrals(F_PDIHS, -105.0, 15.0, 2) },
{ iListInput(2e-4, 1e-8).setHarmonic(F_IDIHS, 100.0, 50.0) },
};
//! Function types for testing polarization. Add new terms at the end.
-std::vector<iListInput> c_InputPols =
-{
+std::vector<iListInput> c_InputPols = {
{ iListInput(2e-5, 1e-8).setPolarization(0.12) },
{ iListInput(1.7e-3, 1e-8).setAnharmPolarization(0.0013, 0.02, 1235.6) },
{ iListInput(1.4e-3, 1e-8).setTholePolarization(0.26, 0.07, 0.09, 1.6) },
};
//! Function types for testing polarization. Add new terms at the end.
-std::vector<iListInput> c_InputRestraints =
-{
+std::vector<iListInput> c_InputRestraints = {
{ iListInput(1e-4, 1e-8).setPDihedrals(F_ANGRES, -100.0, 10.0, 2, -80.0, 20.0) },
{ iListInput(1e-4, 1e-8).setPDihedrals(F_ANGRES, -105.0, 15.0, 2) },
{ iListInput(1e-4, 1e-8).setPDihedrals(F_ANGRESZ, -100.0, 10.0, 2, -80.0, 20.0) },
};
//! Coordinates for testing
-std::vector<std::vector<gmx::RVec> > c_coordinatesForTests =
-{
- {{ 0.0, 0.0, 0.0 }, { 0.0, 0.0, 0.2 }, { 0.005, 0.0, 0.1 }, { -0.001, 0.1, 0.0 }},
- {{ 0.5, 0.0, 0.0 }, { 0.5, 0.0, 0.15 }, { 0.5, 0.07, 0.22 }, { 0.5, 0.18, 0.22 }},
- {{ -0.1143, -0.0282, 0.0 }, { 0.0, 0.0434, 0.0 }, { 0.1185, -0.0138, 0.0 }, { -0.0195, 0.1498, 0.0 }}
+std::vector<std::vector<gmx::RVec>> c_coordinatesForTests = {
+ { { 0.0, 0.0, 0.0 }, { 0.0, 0.0, 0.2 }, { 0.005, 0.0, 0.1 }, { -0.001, 0.1, 0.0 } },
+ { { 0.5, 0.0, 0.0 }, { 0.5, 0.0, 0.15 }, { 0.5, 0.07, 0.22 }, { 0.5, 0.18, 0.22 } },
+ { { -0.1143, -0.0282, 0.0 }, { 0.0, 0.0434, 0.0 }, { 0.1185, -0.0138, 0.0 }, { -0.0195, 0.1498, 0.0 } }
};
//! PBC values for testing
// Those tests give errors with the intel compiler and nothing else, so we disable them only there.
#ifndef __INTEL_COMPILER
-INSTANTIATE_TEST_CASE_P(Bond, ListedForcesTest, ::testing::Combine(::testing::ValuesIn(c_InputBonds), ::testing::ValuesIn(c_coordinatesForTests), ::testing::ValuesIn(c_pbcForTests)));
-
-INSTANTIATE_TEST_CASE_P(Angle, ListedForcesTest, ::testing::Combine(::testing::ValuesIn(c_InputAngles), ::testing::ValuesIn(c_coordinatesForTests), ::testing::ValuesIn(c_pbcForTests)));
-
-INSTANTIATE_TEST_CASE_P(Dihedral, ListedForcesTest, ::testing::Combine(::testing::ValuesIn(c_InputDihs), ::testing::ValuesIn(c_coordinatesForTests), ::testing::ValuesIn(c_pbcForTests)));
-
-INSTANTIATE_TEST_CASE_P(Polarize, ListedForcesTest, ::testing::Combine(::testing::ValuesIn(c_InputPols), ::testing::ValuesIn(c_coordinatesForTests), ::testing::ValuesIn(c_pbcForTests)));
-
-INSTANTIATE_TEST_CASE_P(Restraints, ListedForcesTest, ::testing::Combine(::testing::ValuesIn(c_InputRestraints), ::testing::ValuesIn(c_coordinatesForTests), ::testing::ValuesIn(c_pbcForTests)));
+INSTANTIATE_TEST_CASE_P(Bond,
+ ListedForcesTest,
+ ::testing::Combine(::testing::ValuesIn(c_InputBonds),
+ ::testing::ValuesIn(c_coordinatesForTests),
+ ::testing::ValuesIn(c_pbcForTests)));
+
+INSTANTIATE_TEST_CASE_P(Angle,
+ ListedForcesTest,
+ ::testing::Combine(::testing::ValuesIn(c_InputAngles),
+ ::testing::ValuesIn(c_coordinatesForTests),
+ ::testing::ValuesIn(c_pbcForTests)));
+
+INSTANTIATE_TEST_CASE_P(Dihedral,
+ ListedForcesTest,
+ ::testing::Combine(::testing::ValuesIn(c_InputDihs),
+ ::testing::ValuesIn(c_coordinatesForTests),
+ ::testing::ValuesIn(c_pbcForTests)));
+
+INSTANTIATE_TEST_CASE_P(Polarize,
+ ListedForcesTest,
+ ::testing::Combine(::testing::ValuesIn(c_InputPols),
+ ::testing::ValuesIn(c_coordinatesForTests),
+ ::testing::ValuesIn(c_pbcForTests)));
+
+INSTANTIATE_TEST_CASE_P(Restraints,
+ ListedForcesTest,
+ ::testing::Combine(::testing::ValuesIn(c_InputRestraints),
+ ::testing::ValuesIn(c_coordinatesForTests),
+ ::testing::ValuesIn(c_pbcForTests)));
#endif
-} // namespace
+} // namespace
-} // namespace gmx
+} // namespace gmx
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff