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/dports/science/lammps/lammps-stable_29Sep2021/doc/src/
H A Ddihedral_style.rst27 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 …]
H A Ddihedral_hybrid.rst13 * 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 …]
H A Ddihedral_coeff.rst13 * 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 …]
H A Ddihedral_zero.rst25 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
H A Dcompute_dihedral_local.rst1 .. 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 …]
H A Ddihedral_charmm.rst38 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 …]
H A Dfix_restrain.rst16 * 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 …]
H A Dcompute_dihedral.rst1 .. 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.…
H A Ddihedral_none.rst23 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.
H A Ddihedral_table.rst42 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 …]
/dports/science/rdkit/rdkit-Release_2021_03_5/Code/ForceField/MMFF/
H A DTorsionConstraint.cpp40 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 …]
/dports/science/rdkit/rdkit-Release_2021_03_5/Code/ForceField/UFF/
H A DTorsionConstraint.cpp40 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 …]
/dports/science/py-ase/ase-3.22.0/ase/utils/
H A Dff.py588 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 …]
/dports/science/lammps/lammps-stable_29Sep2021/unittest/force-styles/
H A Dtest_dihedral_style.cpp161 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 …]
/dports/science/lammps/lammps-stable_29Sep2021/src/
H A Dcompute_dihedral.cpp40 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()
/dports/science/py-MDAnalysis/MDAnalysis-0.19.2/MDAnalysis/analysis/
H A Dnuclinfo.py365 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 …]
/dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/MolTransforms/Wrap/
H A DtestMolTransforms.py209 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 …]
/dports/science/p5-PerlMol/PerlMol-0.3500/inc/BUNDLES/Chemistry-Mol-0.35/t/
H A Dgeom.t1 # 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, $v3), 0, "bad dihedral" );
/dports/science/p5-Chemistry-Mol/Chemistry-Mol-0.38/t/
H A Dgeom.t1 # Tests for geometry-related methods such as distance, angle, and dihedral
22 # dihedral
24 is_float( Chemistry::Atom::dihedral_deg(@a), -85.6, 0.1, "dihedral" );
37 is( Chemistry::Atom::dihedral($v0, $v0, $v0, $v0), 0, "bad dihedral" );
38 is( Chemistry::Atom::dihedral($v0, $v1, $v2, $v3), 0, "bad dihedral" );
/dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/MolTransforms/
H A Dtest1.cpp196 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 …]
/dports/science/xtb/xtb-6.4.1/src/
H A Dscanparam.f90281 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 …]
/dports/science/lammps/lammps-stable_29Sep2021/src/KOKKOS/
H A Dverlet_kokkos.cpp140 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 …]
/dports/math/py-Diofant/Diofant-0.13.0/diofant/tests/combinatorics/
H A Dtest_generators.py1 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)) == [
/dports/science/gromacs/gromacs-2021.4/src/gromacs/gmxpreprocess/
H A Dgen_ad.cpp246 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 …]
/dports/math/py-sympy/sympy-1.9/sympy/combinatorics/tests/
H A Dtest_generators.py2 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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