Merge branch 'develop' into cg-dna
This commit is contained in:
Oliver Henrich
94
unittest/force-styles/tests/mol-pair-harmonic_cut.yaml
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94
unittest/force-styles/tests/mol-pair-harmonic_cut.yaml
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---
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lammps_version: 7 Jan 2022
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tags: generated
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date_generated: Sat Jan 15 17:42:24 2022
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epsilon: 5e-14
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skip_tests:
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prerequisites: ! |
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atom full
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pair harmonic/cut
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pre_commands: ! ""
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post_commands: ! |
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pair_modify mix arithmetic
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input_file: in.fourmol
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pair_style: harmonic/cut
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pair_coeff: ! |
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1 1 0.2 2.5
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2 2 0.05 1.0
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2 4 0.05 0.5
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3 3 0.2 3.4
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4 4 0.15 3.1
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5 5 0.15 3.1
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extract: ! |
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k 2
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cut 2
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natoms: 29
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init_vdwl: 0.6229303832094011
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init_coul: 0
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init_stress: ! |2-
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2.7086112336155066e-01 2.7116413086977192e-01 3.9219767031763964e-01 -1.0030847564854772e-01 4.4609473180383268e-02 -4.3637124113592815e-02
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init_forces: ! |2
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1 8.0131849873788189e-03 4.9888010120265600e-02 2.8122360795900539e-02
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2 7.9791227934915224e-03 6.5662021486410233e-03 -9.3912001601608869e-03
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3 -3.0383030044476164e-02 -2.4462070024746502e-02 -6.7080526995988831e-03
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4 -4.2871382862959282e-03 1.2944422156819623e-04 -3.1664690534881235e-03
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5 -2.5653599407787658e-03 -5.6347847352330024e-03 5.7588483204582012e-03
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6 -2.7432516621812987e-02 2.2443342050432843e-02 6.0842119146428050e-03
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7 -2.3732010354850359e-02 4.8925005245008778e-03 -1.0554388509160603e-01
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8 -1.9721449495438432e-02 8.7099489439665806e-03 7.7340656614040257e-02
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9 3.1079843659201794e-03 3.3474898466584100e-03 1.3753907856580455e-02
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10 1.5600383364335340e-02 -3.4154073795756010e-02 -2.4568763191891510e-02
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11 -6.4786170866648325e-04 -2.7187839165446434e-03 -4.0027246972607657e-03
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12 4.5446169193717613e-02 9.5334383719478614e-03 -2.3805265135058946e-02
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13 3.6852167147282842e-03 -1.4578336695269954e-03 -6.9263908097426375e-05
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14 -1.4516812720744084e-03 2.9539789066737132e-04 -3.7646771444256287e-03
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15 -5.4837745225155548e-05 3.7892348244262858e-03 1.3279622443994443e-03
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16 2.7804441490434852e-02 -2.9016569654227675e-02 -2.3977127174652516e-02
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17 -1.3606174403879238e-03 -1.2150893147040220e-02 7.2609480510219010e-02
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18 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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19 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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20 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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21 -2.8478436810585638e-03 -3.4997997565726423e-03 1.0311097670993996e-02
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22 -5.0036838658335881e-03 -1.2125954307909393e-03 -7.8502223695393180e-03
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23 7.8515275468921519e-03 4.7123951873635815e-03 -2.4608753014546784e-03
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24 2.2422341594776187e-03 -9.2864513866737705e-03 5.4147040050256424e-03
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25 -7.0931333559850684e-03 1.1418916865888746e-03 -5.9630640752421178e-03
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26 4.8508991965074497e-03 8.1445597000848954e-03 5.4836007021647544e-04
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27 1.4352981398486984e-03 -1.0223071626521522e-02 3.5886145449699289e-03
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28 -7.4679157140535102e-03 3.2093693544577983e-03 -5.0528642356851916e-03
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29 6.0326175742048118e-03 7.0137022720637250e-03 1.4642496907152625e-03
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run_vdwl: 0.6227892941470253
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run_coul: 0
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run_stress: ! |2-
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2.7079595899259656e-01 2.7106155255810421e-01 3.9199181631609364e-01 -1.0017597886837336e-01 4.4639512685950337e-02 -4.3538044335882868e-02
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run_forces: ! |2
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1 8.0241133736762959e-03 4.9859217970288555e-02 2.8099645116503875e-02
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2 7.9858506322803297e-03 6.5851530052680168e-03 -9.3657942914726639e-03
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3 -3.0378796721416249e-02 -2.4495674709975927e-02 -6.7374520329115941e-03
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4 -4.2659306402640165e-03 1.3406094892709258e-04 -3.1564081120146015e-03
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5 -2.5644106889098472e-03 -5.6291258903991056e-03 5.7537772274397249e-03
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6 -2.7398860728585855e-02 2.2446081967441193e-02 6.0769742046490674e-03
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7 -2.3725250988273959e-02 4.8748360958146379e-03 -1.0543946577300001e-01
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8 -1.9795760001146530e-02 8.7619549352892182e-03 7.7257651402956734e-02
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9 3.1107511049119794e-03 3.3343639112369677e-03 1.3749677634153570e-02
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10 1.5635110483272714e-02 -3.4177809303542570e-02 -2.4562568959156386e-02
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11 -6.4680122415666373e-04 -2.7045376093154955e-03 -3.9833439702283155e-03
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12 4.5410386808201031e-02 9.5232810722562407e-03 -2.3816427499003763e-02
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13 3.6819606745360318e-03 -1.4490090012638590e-03 -6.8397423783681964e-05
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14 -1.4472530230181654e-03 2.8919520744570527e-04 -3.7524156545238243e-03
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15 -5.6155855006963267e-05 3.7938646788886268e-03 1.3339639717048200e-03
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16 2.7787095304862428e-02 -2.9020839215424241e-02 -2.3998357673493245e-02
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17 -1.3560485109625556e-03 -1.2125014062935051e-02 7.2608941832180307e-02
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18 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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19 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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20 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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21 -2.8538862991433229e-03 -3.4800313716197438e-03 1.0305823645864499e-02
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22 -5.0214625596301642e-03 -1.2260879074991976e-03 -7.8500736428379052e-03
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23 7.8753488587734871e-03 4.7061192791189414e-03 -2.4557500030265946e-03
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24 2.2600769444580133e-03 -9.2990099176050046e-03 5.4253104994500942e-03
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25 -7.1247130587123505e-03 1.1308496354809658e-03 -5.9913273289481242e-03
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26 4.8646361142543372e-03 8.1681602821240384e-03 5.6601682949803040e-04
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27 1.4504263375229804e-03 -1.0234012017965840e-02 3.5742943025157811e-03
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28 -7.4838995855112476e-03 3.2116101208619755e-03 -5.0534250649872060e-03
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29 6.0334732479882672e-03 7.0224018971038644e-03 1.4791307624714251e-03
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...
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@ -176,6 +176,33 @@ TEST_F(MoleculeFileTest, minimal)
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ASSERT_THAT(output, MatchesRegex(".*Read molecule template.*1 molecules.*1 atoms.*0 bonds.*"));
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}
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TEST_F(MoleculeFileTest, notype)
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{
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BEGIN_CAPTURE_OUTPUT();
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command("atom_style atomic");
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command("region box block 0 1 0 1 0 1");
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command("create_box 1 box");
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run_mol_cmd(test_name, "", "Comment\n1 atoms\n\n Coords\n\n 1 0.0 0.0 0.0\n");
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auto output = END_CAPTURE_OUTPUT();
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ASSERT_THAT(output, MatchesRegex(".*Read molecule template.*1 molecules.*1 atoms.*0 bonds.*"));
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TEST_FAILURE(".*ERROR: Create_atoms molecule must have atom types.*",
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command("create_atoms 0 single 0.0 0.0 0.0 mol notype 542465"););
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}
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TEST_F(MoleculeFileTest, extramass)
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{
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BEGIN_CAPTURE_OUTPUT();
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command("atom_style atomic");
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command("region box block 0 1 0 1 0 1");
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command("create_box 1 box");
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run_mol_cmd(test_name, "", "Comment\n1 atoms\n\n Coords\n\n 1 0.0 0.0 0.0\n"
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" Types\n\n 1 1\n Masses\n\n 1 1.0\n");
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command("create_atoms 0 single 0.0 0.0 0.0 mol extramass 73546");
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auto output = END_CAPTURE_OUTPUT();
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ASSERT_THAT(output, MatchesRegex(".*WARNING: Molecule attributes do not match "
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"system attributes.*"));
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}
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TEST_F(MoleculeFileTest, twomols)
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{
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BEGIN_CAPTURE_OUTPUT();
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@ -356,18 +356,16 @@ create_atoms 1 single &
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def test_extract_box_triclinic(self):
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self.lmp.command("boundary p p p")
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self.lmp.command("region box block 0 2 0 2 0 2")
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self.lmp.command("region box prism 0 2 0 2 0 2 0.1 0.2 0.3")
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self.lmp.command("create_box 1 box")
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self.lmp.command("change_box all triclinic")
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self.lmp.command("change_box all xy final 0.1 yz final 0.2 xz final 0.3")
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boxlo, boxhi, xy, yz, xz, periodicity, box_change = self.lmp.extract_box()
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self.assertEqual(boxlo, [0.0, 0.0, 0.0])
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self.assertEqual(boxhi, [2.0, 2.0, 2.0])
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self.assertEqual(xy, 0.1)
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self.assertEqual(yz, 0.2)
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self.assertEqual(xz, 0.3)
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self.assertEqual(xz, 0.2)
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self.assertEqual(yz, 0.3)
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self.assertEqual(periodicity, [1, 1, 1])
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self.assertEqual(box_change, 0)
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