/dports/science/lammps/lammps-stable_29Sep2021/doc/src/ |
H A D | dihedral_style.rst | 27 Set the formula(s) LAMMPS uses to compute dihedral interactions 34 potentials can be setup using the *hybrid* dihedral style. 51 When both a dihedral and pair style is defined, the 74 dihedral styles with dihedral equations defined by other force fields, 78 dihedral equation applies to each individual dihedral. Thus you need 96 The individual style names on the :ref:`Commands dihedral <dihedral>` page are followed by one or 103 * :doc:`charmm <dihedral_charmm>` - CHARMM dihedral 108 * :doc:`harmonic <dihedral_harmonic>` - harmonic dihedral 109 * :doc:`helix <dihedral_helix>` - helix dihedral 112 * :doc:`opls <dihedral_opls>` - OPLS dihedral [all …]
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H A D | dihedral_hybrid.rst | 13 * style1,style2 = list of one or more dihedral styles 27 The *hybrid* style enables the use of multiple dihedral styles in one 28 simulation. An dihedral style is assigned to each dihedral type. For 29 example, dihedrals in a polymer flow (of dihedral type 1) could be 31 boundary (of dihedral type 2) could be computed with a *helix* 32 potential. The assignment of dihedral type to style is made via the 38 dihedral_coeff commands set dihedrals of dihedral type 1 to be 61 file for dihedral types that are not *class2*, you must use an 62 dihedral style of *skip* as a placeholder, e.g. 79 for specific dihedral types. [all …]
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H A D | dihedral_coeff.rst | 13 * N = dihedral type (see asterisk form below) 14 * args = coefficients for one or more dihedral types 28 Specify the dihedral force field coefficients for one or more dihedral types. 29 The number and meaning of the coefficients depends on the dihedral style. 43 for the same dihedral type. For example, these commands set the coeffs 44 for all dihedral types, then overwrite the coeffs for just dihedral type 2: 70 dihedral styles with dihedral equations defined by other force fields, 74 dihedral equation applies to each individual dihedral. Thus you need 80 The list of all dihedral styles defined in LAMMPS is given on the 82 in more compact form on the :ref:`Commands dihedral <dihedral>` doc page. [all …]
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H A D | dihedral_zero.rst | 25 Using a dihedral style of zero means dihedral forces and energies are 26 not computed, but the geometry of dihedral quadruplets is still 29 As an example, the :doc:`compute dihedral/local <compute_dihedral_local>` command can be used to 30 compute the theta values for the list of quadruplets of dihedral atoms 32 command. If no dihedral style is defined, this command cannot be 36 section for any dihedral style. Similarly, any dihedral_coeff commands 37 will only be checked for the dihedral type number and the rest ignored. 40 used for all dihedral types, though no additional values are
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H A D | compute_dihedral_local.rst | 1 .. index:: compute dihedral/local 3 compute dihedral/local command 11 compute ID group-ID dihedral/local value1 value2 ... keyword args ... 14 * dihedral/local = style name of this compute command 20 *phi* = tabulate dihedral angles 37 compute 1 all dihedral/local phi 39 compute 1 all dihedral/local phi v_cos set phi p 49 The value *phi* is the dihedral angle, as defined in the diagram on 53 compute a user-specified function of the dihedral angle phi. The 76 compute 2 all dihedral/local phi v_cos v_cossq set phi p [all …]
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H A D | dihedral_charmm.rst | 38 The *charmm* and *charmmfsw* dihedral styles use the potential 45 force field. This dihedral style can also be used for the AMBER force 72 when using the CHARMM dihedral style with non-CHARMM force fields. 74 atoms in a dihedral are skipped during the normal non-bonded force 75 computation and instead evaluated as part of the dihedral using 80 (once for the clockwise 1-4 pair in dihedral 1-2-3-4 and once in the 81 counterclockwise dihedral 1-6-5-4) and thus the weighting factor has 87 Note that this dihedral weighting factor is unrelated to the scaling 92 computed with the dihedral. This means that if any of the weighting 93 factors defined as dihedral coefficients (fourth coeff above) are [all …]
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H A D | fix_restrain.rst | 16 * keyword = *bond* or *lbound* or *angle* or *dihedral* 39 phi0 = equilibrium dihedral angle phi (degrees) 50 fix holdem all restrain dihedral 1 2 3 4 2000.0 2000.0 120.0 52 …fix texas_holdem all restrain dihedral 1 2 3 4 0.0 2000.0 120.0 dihedral 1 2 3 5 0.0 2000.0 -120.0… 60 creating a bond or angle or dihedral for the same atoms in a data 74 Adding a bond/angle/dihedral with this command does not apply 87 to multiple dihedral angles using a restraint coefficient that 120 fix REST all restrain dihedral 2 1 3 8 0.0 5000.0 ${angle1} dihedral 3 1 2 9 0.0 5000.0 ${angle2} 124 …fix REST all restrain dihedral 2 1 3 8 5000.0 5000.0 ${angle1} dihedral 3 1 2 9 5000.0 5000.0 ${an… 196 The *dihedral* keyword applies a dihedral restraint to the specified [all …]
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H A D | compute_dihedral.rst | 1 .. index:: compute dihedral 3 compute dihedral command 11 compute ID group-ID dihedral 14 * dihedral = style name of this compute command 21 compute 1 all dihedral 26 Define a computation that extracts the dihedral energy calculated by 27 each of the dihedral sub-styles used in the :doc:`dihedral_style hybrid <dihedral_hybrid>` command.…
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H A D | dihedral_none.rst | 23 Using a dihedral style of none means dihedral forces and energies are 24 not computed, even if quadruplets of dihedral atoms were listed in the 28 calculate dihedral statistics, but compute no dihedral interactions.
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H A D | dihedral_table.rst | 42 The *table* and *table/cut* dihedral styles create interpolation tables 44 in a file(s) as a function of the dihedral angle "phi". The files are 46 dihedral style *table/cut* additionally an analytic cutoff that is 48 the dihedral interaction. 52 *Ntable* dihedral angles. During a simulation, these tables are used 57 For the *linear* style, the dihedral angle (phi) is used to find 2 79 For dihedral style *table/cut* the following coefficients must be 80 defined for each dihedral type via the :doc:`dihedral_coeff 90 The cutoff dihedral style uses a tabulated dihedral interaction with a 107 to zero. The value of zero effectively "turns off" the dihedral [all …]
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/dports/science/rdkit/rdkit-Release_2021_03_5/Code/ForceField/MMFF/ |
H A D | TorsionConstraint.cpp | 40 double dihedralTarget = dihedral; in computeDihedralTerm() 41 if (!(dihedral > d_minDihedralDeg && dihedral < d_maxDihedralDeg) && in computeDihedralTerm() 54 double dihedralTerm = dihedral - dihedralTarget; in computeDihedralTerm() 92 double dihedral; in TorsionConstraintContrib() local 95 dihedral *= RAD2DEG; in TorsionConstraintContrib() 96 minDihedralDeg += dihedral; in TorsionConstraintContrib() 97 maxDihedralDeg += dihedral; in TorsionConstraintContrib() 106 double dihedral; in getEnergy() local 109 dihedral *= RAD2DEG; in getEnergy() 127 double dihedral; in getGrad() local [all …]
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/dports/science/rdkit/rdkit-Release_2021_03_5/Code/ForceField/UFF/ |
H A D | TorsionConstraint.cpp | 40 double dihedralTarget = dihedral; in computeDihedralTerm() 41 if (!(dihedral > d_minDihedralDeg && dihedral < d_maxDihedralDeg) && in computeDihedralTerm() 54 double dihedralTerm = dihedral - dihedralTarget; in computeDihedralTerm() 92 double dihedral; in TorsionConstraintContrib() local 95 dihedral *= RAD2DEG; in TorsionConstraintContrib() 96 minDihedralDeg += dihedral; in TorsionConstraintContrib() 97 maxDihedralDeg += dihedral; in TorsionConstraintContrib() 106 double dihedral; in getEnergy() local 109 dihedral *= RAD2DEG; in getEnergy() 127 double dihedral; in getGrad() local [all …]
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/dports/science/py-ase/ase-3.22.0/ase/utils/ |
H A D | ff.py | 588 v = dihedral.k*(1.0 + np.cos(dihedral.n*d - dihedral.d0)) 590 dihedral.d = d 641 gx *= -dihedral.k*dihedral.n*np.sin(dihedral.n*d - dihedral.d0) 643 dihedral.d = d 655 dihedral_eps = Dihedral(dihedral.atomi, dihedral.atomj, 656 dihedral.atomk, dihedral.atoml, 657 dihedral.k, dihedral.d0, dihedral.n) 679 Hx *= ( np.exp(dihedral.alpha[0]*(dihedral.rref[0]**2-dij**2)) 748 Hx = ( np.abs(-dihedral.k*dihedral.n**2 775 dihedral.d = d [all …]
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/dports/science/lammps/lammps-stable_29Sep2021/unittest/force-styles/ |
H A D | test_dihedral_style.cpp | 161 if (!lmp->force->dihedral) { in restart_lammps() 356 auto dihedral = lmp->force->dihedral; in TEST() local 377 stress = dihedral->virial; in TEST() 389 stress = dihedral->virial; in TEST() 424 dihedral = lmp->force->dihedral; in TEST() 487 dihedral = lmp->force->dihedral; in TEST() 517 dihedral = lmp->force->dihedral; in TEST() 586 auto dihedral = lmp->force->dihedral; in TEST() local 608 stress = dihedral->virial; in TEST() 620 stress = dihedral->virial; in TEST() [all …]
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/dports/science/lammps/lammps-stable_29Sep2021/src/ |
H A D | compute_dihedral.cpp | 40 dihedral = (DihedralHybrid *) force->dihedral_match("hybrid"); in ComputeDihedral() 41 if (!dihedral) in ComputeDihedral() 44 size_vector = nsub = dihedral->nstyles; in ComputeDihedral() 64 dihedral = (DihedralHybrid *) force->dihedral_match("hybrid"); in init() 65 if (!dihedral) in init() 68 if (dihedral->nstyles != nsub) in init() 81 emine[i] = dihedral->styles[i]->energy; in compute_vector()
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/dports/science/py-MDAnalysis/MDAnalysis-0.19.2/MDAnalysis/analysis/ |
H A D | nuclinfo.py | 365 data1 = angle1.dihedral.value() 366 data2 = angle2.dihedral.value() 367 data3 = angle3.dihedral.value() 368 data4 = angle4.dihedral.value() 369 data5 = angle5.dihedral.value() 456 beta = b.dihedral.value() % 360 460 zeta = z.dihedral.value() % 360 461 chi = c.dihedral.value() % 360 522 beta = b.dihedral.value() % 360 642 zeta = z.dihedral.value() % 360 [all …]
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/dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/MolTransforms/Wrap/ |
H A D | testMolTransforms.py | 209 self.failUnlessAlmostEqual(dihedral, 176.05, 2) 211 dihedral = rdmt.GetDihedralDeg(conf, 8, 0, 19, 21) 212 self.failUnlessAlmostEqual(dihedral, 65.0, 1) 215 self.failUnlessAlmostEqual(dihedral, -130.0, 1) 220 self.failUnlessAlmostEqual(dihedral, -120.0, 1) 229 dihedral = rdmt.GetDihedralDeg(conf, 6, 1, 2, 9) 230 self.failUnlessAlmostEqual(dihedral, 0.0, 1) 233 dihedral = rdmt.GetDihedralDeg(conf, 6, 1, 2, 9) 234 self.failUnlessAlmostEqual(dihedral, 120.0, 1) 238 dihedral = rdmt.GetDihedralDeg(conf, 6, 1, 2, 9) [all …]
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/dports/science/p5-PerlMol/PerlMol-0.3500/inc/BUNDLES/Chemistry-Mol-0.35/t/ |
H A D | geom.t | 1 # Tests for geometry-related methods such as distance, angle, and dihedral 22 # dihedral 24 is_float( Chemistry::Atom::dihedral_deg(@a), -85.6, 0.1, "dihedral" ); 37 is( Chemistry::Atom::dihedral($v0, $v0, $v0, $v0), 0, "bad dihedral" ); 38 is( Chemistry::Atom::dihedral($v0, $v1, $v2, $v3), 0, "bad dihedral" );
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/dports/science/p5-Chemistry-Mol/Chemistry-Mol-0.38/t/ |
H A D | geom.t | 1 # Tests for geometry-related methods such as distance, angle, and dihedral 22 # dihedral 24 is_float( Chemistry::Atom::dihedral_deg(@a), -85.6, 0.1, "dihedral" ); 37 is( Chemistry::Atom::dihedral($v0, $v0, $v0, $v0), 0, "bad dihedral" ); 38 is( Chemistry::Atom::dihedral($v0, $v1, $v2, $v3), 0, "bad dihedral" );
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/dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/MolTransforms/ |
H A D | test1.cpp | 196 dihedral = getDihedralDeg(conf, 8, 0, 19, 21); in testGetSetDihedral() 197 TEST_ASSERT(RDKit::feq(dihedral, 65.0)); in testGetSetDihedral() 199 dihedral = getDihedralDeg(conf, 8, 0, 19, 21); in testGetSetDihedral() 200 TEST_ASSERT(RDKit::feq(dihedral, -130.0)); in testGetSetDihedral() 202 dihedral = getDihedralRad(conf, 8, 0, 19, 21); in testGetSetDihedral() 205 TEST_ASSERT(RDKit::feq(dihedral, -120.0)); in testGetSetDihedral() 218 TEST_ASSERT(RDKit::feq(dihedral, 0.0)); in testGetSetDihedralThroughTripleBond() 221 dihedral = getDihedralDeg(conf, 6, 1, 2, 9); in testGetSetDihedralThroughTripleBond() 222 TEST_ASSERT(RDKit::feq(dihedral, 120.0)); in testGetSetDihedralThroughTripleBond() 226 dihedral = getDihedralDeg(conf, 6, 1, 2, 9); in testGetSetDihedralThroughTripleBond() [all …]
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/dports/science/xtb/xtb-6.4.1/src/ |
H A D | scanparam.f90 | 281 if (potset%dihedral%n.gt.0) then 286 do m = 1, potset%dihedral%n 288 i = potset%dihedral%atoms(mm) 289 j = potset%dihedral%atoms(mm+1) 290 k = potset%dihedral%atoms(mm+2) 291 l = potset%dihedral%atoms(mm+3) 292 val0 = potset%dihedral%val(m) 303 potset%dihedral%fc 305 potset%dihedral%fc/4.0_wp 427 potset%dihedral%n = potset%dihedral%n+1 [all …]
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/dports/science/lammps/lammps-stable_29Sep2021/src/KOKKOS/ |
H A D | verlet_kokkos.cpp | 140 if (force->dihedral) { in setup() 141 atomKK->sync(force->dihedral->execution_space,force->dihedral->datamask_read); in setup() 142 force->dihedral->compute(eflag,vflag); in setup() 143 atomKK->modified(force->dihedral->execution_space,force->dihedral->datamask_modify); in setup() 229 if (force->dihedral) { in setup_minimal() 230 atomKK->sync(force->dihedral->execution_space,force->dihedral->datamask_read); in setup_minimal() 231 force->dihedral->compute(eflag,vflag); in setup_minimal() 232 atomKK->modified(force->dihedral->execution_space,force->dihedral->datamask_modify); in setup_minimal() 413 if (atomKK->molecular && force->dihedral) { in run() 475 if (force->dihedral) { in run() [all …]
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/dports/math/py-Diofant/Diofant-0.13.0/diofant/tests/combinatorics/ |
H A D | test_generators.py | 1 from diofant.combinatorics import (Permutation, alternating, cyclic, dihedral, 78 assert list(dihedral(1)) == [ 81 assert list(dihedral(2)) == [ 87 assert list(dihedral(3)) == [ 95 assert list(dihedral(5)) == [
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/dports/science/gromacs/gromacs-2021.4/src/gromacs/gmxpreprocess/ |
H A D | gen_ad.cpp | 246 for (const auto& dihedral : dih) in clean_dih() local 259 for (auto dihedral = dih.begin(); dihedral != dih.end(); dihedral++) in clean_dih() local 264 if (was_dihedral_set_in_rtp(*dihedral) || dihedral == dih.begin() in clean_dih() 265 || !is_dihedral_on_same_bond(*dihedral, *(dihedral - 1))) in clean_dih() 272 for (auto dihedral = newDihedrals.begin(); dihedral != newDihedrals.end();) in clean_dih() local 295 int bestl = dihedral->second; in clean_dih() 300 int next = dihedral->second + 1; in clean_dih() 301 for (int l = dihedral->second; in clean_dih() 315 dihedral->first = dih[bestl]; in clean_dih() 319 ++dihedral; in clean_dih() [all …]
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/dports/math/py-sympy/sympy-1.9/sympy/combinatorics/tests/ |
H A D | test_generators.py | 2 dihedral, rubik 76 assert list(dihedral(1)) == [ 79 assert list(dihedral(2)) == [ 85 assert list(dihedral(3)) == [ 93 assert list(dihedral(5)) == [
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