Home
last modified time | relevance | path

Searched refs:atoms (Results 1 – 25 of 5309) sorted by relevance

12345678910>>...213

/dports/x11-toolkits/gnustep-back/libs-back-back-0_28_0/Headers/x11/
H A DXGGeneric.h120 #define TEXT_ATOM atoms[0]
121 #define UTF8_STRING_ATOM atoms[1]
122 #define WM_PROTOCOLS_ATOM atoms[2]
123 #define WM_TAKE_FOCUS_ATOM atoms[3]
124 #define WM_DELETE_WINDOW_ATOM atoms[4]
125 #define WM_STATE_ATOM atoms[5]
126 #define _NET_WM_PING_ATOM atoms[6]
127 #define _NET_WM_SYNC_REQUEST_ATOM atoms[7]
128 #define _NET_WM_SYNC_REQUEST_COUNTER_ATOM atoms[8]
129 #define _NET_WM_WINDOW_TYPE_ATOM atoms[9]
[all …]
/dports/math/py-cvxpy/cvxpy-1.1.17/cvxpy/atoms/
H A D__init__.py19 from cvxpy.atoms.affine.bmat import bmat
20 from cvxpy.atoms.affine.conj import conj
21 from cvxpy.atoms.affine.conv import conv
23 from cvxpy.atoms.affine.diag import diag
31 from cvxpy.atoms.affine.sum import sum
35 from cvxpy.atoms.affine.vec import vec
37 from cvxpy.atoms.cummax import cummax
74 from cvxpy.atoms.max import max
75 from cvxpy.atoms.min import min
78 from cvxpy.atoms.norm1 import norm1
[all …]
/dports/science/nwchem-data/nwchem-7.0.2-release/src/basis/
H A Dlibrary.fam1 Basis Set "STO-2G" (number of atoms 20)
2 Basis Set "STO-3G" (number of atoms 52)
3 Basis Set "STO-6G" (number of atoms 36)
4 Basis Set "STO-3G*" (number of atoms 18)
5 Basis Set "3-21G" (number of atoms 55)
6 Basis Set "3-21++G" (number of atoms 18)
7 Basis Set "3-21G*" (number of atoms 17)
9 Basis Set "3-21GSP" (number of atoms 18)
10 Basis Set "4-22GSP" (number of atoms 18)
11 Basis Set "4-31G" (number of atoms 13)
[all …]
/dports/science/nwchem/nwchem-7b21660b82ebd85ef659f6fba7e1e73433b0bd0a/src/basis/
H A Dlibrary.fam1 Basis Set "STO-2G" (number of atoms 20)
2 Basis Set "STO-3G" (number of atoms 52)
3 Basis Set "STO-6G" (number of atoms 36)
4 Basis Set "STO-3G*" (number of atoms 18)
5 Basis Set "3-21G" (number of atoms 55)
6 Basis Set "3-21++G" (number of atoms 18)
7 Basis Set "3-21G*" (number of atoms 17)
9 Basis Set "3-21GSP" (number of atoms 18)
10 Basis Set "4-22GSP" (number of atoms 18)
11 Basis Set "4-31G" (number of atoms 13)
[all …]
/dports/science/py-pyscf/pyscf-2.0.1/pyscf/symm/test/
H A Dtest_geom.py35 atoms = atoms[5:]
40 atoms = geom.shift_atom(atoms, orig, axes)
47 atoms = atoms[5:]
53 atoms = geom.shift_atom(atoms, orig, axes)
61 atoms = atoms[6:]
65 atoms = geom.shift_atom(atoms, orig, axes)
72 atoms = atoms[6:]
79 atoms = geom.shift_atom(atoms, orig, axes)
86 atoms = atoms[6:]
93 atoms = geom.shift_atom(atoms, orig, axes)
[all …]
/dports/science/py-ase/ase-3.22.0/ase/test/calculator/
H A Dtest_lj.py18 atoms.calc = calc
19 yield atoms
22 atoms.calc = calc
23 yield atoms
46 atoms.calc.calculate(atoms, system_changes=['positions'])
57 atoms.calc = calc
74 atoms.set_cell(atoms.cell * stretch, scale_atoms=True)
79 yield atoms
82 atoms.set_cell(atoms.cell * stretch, scale_atoms=True)
88 yield atoms
[all …]
/dports/science/openmx/openmx3.8/work/nbo_example/
H A DSiO2_NAO.std33 <Input_std> The system includes 2 species and 648 atoms.
63 Allocation of atoms to proccesors at MD_iter= 1
66 proc = 0 # of atoms= 1 estimated weight= 1.00000
67 proc = 1 # of atoms= 1 estimated weight= 1.00000
68 proc = 2 # of atoms= 1 estimated weight= 1.00000
69 proc = 3 # of atoms= 1 estimated weight= 1.00000
70 proc = 4 # of atoms= 1 estimated weight= 1.00000
71 proc = 5 # of atoms= 1 estimated weight= 1.00000
72 proc = 6 # of atoms= 1 estimated weight= 1.00000
1726 ### Natural populations of target atoms ###
[all …]
/dports/science/apbs/apbs-pdb2pqr-apbs-1.5-102-g500c1473/pdb2pqr/pdb2pka/
H A Dligand_topology.py39 self.atoms={}
78 atoms=self.atoms.keys()
119 self.atoms[name]['nbds'] = len(self.atoms[name]['lBonds'])
121 self.atoms[name]['nbhyd'] = self.atoms[name]['nbds']- self.atoms[name]['nbhvy']
127 atoms=self.atoms.keys()
146 atoms=self.atoms.keys()
236 atoms=self.atoms.keys()
237 atoms.sort()
318 atoms=self.atoms.keys()
319 atoms.sort()
[all …]
/dports/science/py-ase/ase-3.22.0/ase/test/
H A Dtest_symbols.py8 def atoms(): function
13 def symbols(atoms): argument
14 return atoms.symbols
18 print(atoms.symbols)
19 atoms.symbols[0] = 'X'
29 print(atoms)
30 print(atoms.numbers)
34 assert atoms.get_chemical_symbols() == list(atoms.symbols)
46 print(atoms.symbols)
50 def test_search(atoms): argument
[all …]
/dports/www/bolt/bolt-2.2.24/vendor/bolt/pathogen/src/
H A DAbstractPath.php53 $this->atoms = $this->normalizeAtoms($atoms);
100 $atoms = $this->atoms();
122 $atoms = $this->atoms();
179 $atoms = $this->atoms();
653 $atoms = iterator_to_array($atoms);
657 array_merge($this->atoms(), $atoms),
781 $atoms = $this->atoms();
793 $atoms,
808 $atoms = $this->atoms();
886 array_splice($atoms, 1, count($atoms), $replacement);
[all …]
/dports/science/cdk/cdk-cdk-2.3/tool/hash/src/test/java/org/openscience/cdk/hash/
H A DPerturbedAtomHashGeneratorTest.java91 …IBond[] bonds = new IBond[]{new Bond(atoms[0], atoms[1], SINGLE), new Bond(atoms[0], atoms[4], SIN… in cyclopentylcyclopentane()
92 new Bond(atoms[1], atoms[2], SINGLE), new Bond(atoms[2], atoms[3], SINGLE), in cyclopentylcyclopentane()
93 new Bond(atoms[3], atoms[4], SINGLE), new Bond(atoms[5], atoms[6], SINGLE), in cyclopentylcyclopentane()
94 new Bond(atoms[5], atoms[9], SINGLE), new Bond(atoms[6], atoms[7], SINGLE), in cyclopentylcyclopentane()
95 new Bond(atoms[7], atoms[8], SINGLE), new Bond(atoms[8], atoms[9], SINGLE), in cyclopentylcyclopentane()
96 new Bond(atoms[8], atoms[0], SINGLE),}; in cyclopentylcyclopentane()
109 …IBond[] bonds = new IBond[]{new Bond(atoms[0], atoms[1], SINGLE), new Bond(atoms[0], atoms[5], SIN… in decahydronaphthalene()
110 new Bond(atoms[1], atoms[2], SINGLE), new Bond(atoms[2], atoms[3], SINGLE), in decahydronaphthalene()
111 new Bond(atoms[3], atoms[4], SINGLE), new Bond(atoms[6], atoms[5], SINGLE), in decahydronaphthalene()
112 new Bond(atoms[5], atoms[4], SINGLE), new Bond(atoms[4], atoms[7], SINGLE), in decahydronaphthalene()
[all …]
/dports/multimedia/libquicktime-lame/libquicktime-1.2.4/src/
H A Duseratoms.c45 u->atoms[i][3]; in quicktime_user_atoms_get_atom()
46 return u->atoms[i]; in quicktime_user_atoms_get_atom()
56 u->atoms = in quicktime_user_atoms_add_atom()
57 realloc(u->atoms, (u->num_atoms+1)*sizeof(*u->atoms)); in quicktime_user_atoms_add_atom()
79 u->atoms = in quicktime_user_atoms_read_atom()
80 realloc(u->atoms, (u->num_atoms+1)*sizeof(*u->atoms)); in quicktime_user_atoms_read_atom()
101 if(u->atoms) in quicktime_user_atoms_delete()
105 free(u->atoms[i]); in quicktime_user_atoms_delete()
107 free(u->atoms); in quicktime_user_atoms_delete()
185 u->atoms[i][3]; in quicktime_user_atoms_dump()
[all …]
/dports/multimedia/libquicktime/libquicktime-1.2.4/src/
H A Duseratoms.c45 u->atoms[i][3]; in quicktime_user_atoms_get_atom()
46 return u->atoms[i]; in quicktime_user_atoms_get_atom()
56 u->atoms = in quicktime_user_atoms_add_atom()
57 realloc(u->atoms, (u->num_atoms+1)*sizeof(*u->atoms)); in quicktime_user_atoms_add_atom()
79 u->atoms = in quicktime_user_atoms_read_atom()
80 realloc(u->atoms, (u->num_atoms+1)*sizeof(*u->atoms)); in quicktime_user_atoms_read_atom()
101 if(u->atoms) in quicktime_user_atoms_delete()
105 free(u->atoms[i]); in quicktime_user_atoms_delete()
107 free(u->atoms); in quicktime_user_atoms_delete()
185 u->atoms[i][3]; in quicktime_user_atoms_dump()
[all …]
/dports/science/p5-PerlMol/PerlMol-0.3500/inc/BUNDLES/Chemistry-Reaction-0.02/lib/Chemistry/
H A DReaction.pm166 my @atoms = $bond->atoms;
167 @atoms[0,1] = @atoms[1,0] unless $atoms[0] lt $atoms[1];
168 $bonds{$atoms[0]}{$atoms[1]} = [$bond->order];
177 my @atoms = $bond->atoms;
180 @atoms[0,1] = @atoms[1,0] unless $atoms[0] lt $atoms[1];
206 my @atoms = $bond->atoms;
207 my @a = @{$bonds{$atoms[0]}{$atoms[1]}};
217 my @atoms = $bond->atoms;
220 @atoms[0,1] = @atoms[1,0] unless $atoms[0] lt $atoms[1];
315 my @atoms = $bond->atoms;
[all …]
/dports/science/p5-Chemistry-Reaction/Chemistry-Reaction-0.02/lib/Chemistry/
H A DReaction.pm166 my @atoms = $bond->atoms;
167 @atoms[0,1] = @atoms[1,0] unless $atoms[0] lt $atoms[1];
168 $bonds{$atoms[0]}{$atoms[1]} = [$bond->order];
177 my @atoms = $bond->atoms;
180 @atoms[0,1] = @atoms[1,0] unless $atoms[0] lt $atoms[1];
206 my @atoms = $bond->atoms;
207 my @a = @{$bonds{$atoms[0]}{$atoms[1]}};
217 my @atoms = $bond->atoms;
220 @atoms[0,1] = @atoms[1,0] unless $atoms[0] lt $atoms[1];
315 my @atoms = $bond->atoms;
[all …]
/dports/science/cdk/cdk-cdk-2.3/legacy/src/main/java/org/openscience/cdk/smsd/ring/
H A DPathEdge.java69 private List<IAtom> atoms; field in PathEdge
72 this.atoms = atoms; in PathEdge()
76 return atoms; in getAtoms()
80 return atoms.get(0); in getSource()
84 return atoms.get(atoms.size() - 1); in getTarget()
88 return (atoms.size() > 2) && atoms.get(0).equals(atoms.get(atoms.size() - 1)); in isCycle()
123 if (atoms.get(i) == atoms.get(j)) { in isRealPath()
133 if (atoms.get(atoms.size() - 1) == others.get(0) in getIntersection()
134 || atoms.get(atoms.size() - 1) == others.get(others.size() - 1)) { in getIntersection()
135 return atoms.get(atoms.size() - 1); in getIntersection()
[all …]
/dports/math/scilab/scilab-6.1.1/scilab/modules/atoms/locales/
H A Datoms.pot1 # Localization of the module atoms
20 # File: modules/atoms/macros/atomsAutoload.sci, line: 50
21 # File: modules/atoms/macros/atomsLoad.sci, line: 41
39 # File: modules/atoms/macros/atomsSearch.sci, line: 31
71 # File: modules/atoms/macros/atomsLoad.sci, line: 45
72 # File: modules/atoms/macros/atomsRemove.sci, line: 49
77 # File: modules/atoms/macros/atomsShow.sci, line: 38
78 # File: modules/atoms/macros/atomsTest.sci, line: 42
79 # File: modules/atoms/macros/atomsTest.sci, line: 50
80 # File: modules/atoms/macros/atomsUpdate.sci, line: 49
[all …]
/dports/x11-wm/jwm/jwm-2.3.7/src/
H A Dhint.c68 Atom atoms[ATOM_COUNT]; variable
112 { &atoms[ATOM_NET_WM_STATE_DEMANDS_ATTENTION],
124 { &atoms[ATOM_NET_WM_ACTION_CHANGE_DESKTOP],
149 { &atoms[ATOM_NET_WM_WINDOW_TYPE_NOTIFICATION],
160 { &atoms[ATOM_NET_SYSTEM_TRAY_ORIENTATION],
168 { &atoms[ATOM_JWM_WM_STATE_MAXIMIZED_TOP],
170 { &atoms[ATOM_JWM_WM_STATE_MAXIMIZED_BOTTOM],
172 { &atoms[ATOM_JWM_WM_STATE_MAXIMIZED_LEFT],
174 { &atoms[ATOM_JWM_WM_STATE_MAXIMIZED_RIGHT],
217 supported[x - FIRST_NET_ATOM] = atoms[x]; in StartupHints()
[all …]
/dports/science/madness/madness-ebb3fd7/src/apps/chem/
H A Dmolecule.cc290 atoms[i].x, atoms[i].y, atoms[i].z); in print()
300 return distance(atoms[i].x, atoms[i].y, atoms[i].z, in inter_atomic_distance()
301 atoms[j].x, atoms[j].y, atoms[j].z); in inter_atomic_distance()
459 xx += atoms[i].x*atoms[i].q; in center()
517 double x=atoms[i].x, y=atoms[i].y, z=atoms[i].z; in test_for_op()
546 double r[3] = {atoms[i].x, atoms[i].y, atoms[i].z}; in swapaxes()
548 atoms[i].x=r[0]; atoms[i].y=r[1]; atoms[i].z=r[2]; in swapaxes()
649 double q = atoms[i].mass, x[3] = {atoms[i].x, atoms[i].y, atoms[i].z}; in moment_of_inertia()
667 double q = atoms[i].atomic_number, x[3] = {atoms[i].x, atoms[i].y, atoms[i].z}; in orient()
713 r[0]=atoms[i].x; r[1]=atoms[i].y, r[2]= atoms[i].z; in rotate()
[all …]
/dports/science/py-ase/ase-3.22.0/ase/test/calculator/abinit/
H A Dtest_main.py20 def run(atoms): argument
21 atoms.get_forces()
39 atoms = bulk('Si')
40 atoms.calc = factory.calc(nbands=4 * len(atoms), kpts=[4, 4, 4])
41 run(atoms)
59 run(atoms)
69 return atoms
87 run(atoms)
94 run(atoms)
106 atoms.calc = factory.calc(nbands=len(atoms) * 7, kpts=[8, 8, 8])
[all …]
/dports/science/gromacs/gromacs-2021.4/src/gromacs/trajectoryanalysis/tests/
H A Dtopologyinformation.cpp112 auto atoms = topInfo.atoms(); in runCommonTests() local
144 EXPECT_TRUE(atoms->haveMass); in TEST()
154 EXPECT_FALSE(atoms->pdbinfo); in TEST()
155 EXPECT_EQ(10, atoms->nres); in TEST()
156 ASSERT_TRUE(atoms->resinfo); in TEST()
177 EXPECT_TRUE(atoms->haveMass); in TEST()
187 ASSERT_TRUE(atoms->pdbinfo); in TEST()
188 EXPECT_EQ(10, atoms->nres); in TEST()
189 ASSERT_TRUE(atoms->resinfo); in TEST()
239 EXPECT_EQ(10, atoms->nres); in TEST()
[all …]
/dports/science/v_sim/v_sim-3.8.0/src/coreTools/
H A Datoms_yaml.c259 … atoms->rxyz[3 * i + 0], atoms->rxyz[3 * i + 1], atoms->rxyz[3 * i + 2], atoms->iatype[i], in posinp_atoms_trace()
260 atoms->ifrztyp[i], atoms->igspin[i], atoms->igchg[i]); in posinp_atoms_trace()
267 atoms->fxyz[3 * i + 0], atoms->fxyz[3 * i + 1], atoms->fxyz[3 * i + 2]); in posinp_atoms_trace()
1083 atoms->rxyz = realloc(atoms->rxyz, sizeof(double) * 3 * atoms->nat); in posinp_yaml_coords()
1084 atoms->iatype = realloc(atoms->iatype, sizeof(unsigned int) * atoms->nat); in posinp_yaml_coords()
1093 atoms->igspin = realloc(atoms->igspin, sizeof(int) * atoms->nat); in posinp_yaml_coords()
1100 atoms->igchg = realloc(atoms->igchg, sizeof(int) * atoms->nat); in posinp_yaml_coords()
1106 for (atoms->ntypes = 0; atoms->atomnames[atoms->ntypes]; atoms->ntypes++); in posinp_yaml_coords()
1107 atoms->props = realloc(atoms->props, sizeof(PosinpDict) * atoms->nat); in posinp_yaml_coords()
1108 atoms->atomnames = realloc(atoms->atomnames, sizeof(char*) * atoms->ntypes); in posinp_yaml_coords()
[all …]
/dports/science/py-ase/ase-3.22.0/ase/test/constraints/
H A Dtest_fixinternals.py27 atoms.rattle(stdev=0.3)
28 return atoms
32 atoms = setup_atoms()
67 opt = BFGS(atoms)
77 atoms.calc = calc
78 atoms.set_constraint(constr)
104 atoms = setup_atoms()
143 atoms.calc = EMT()
146 opt = BFGS(atoms)
173 constr.index_shuffle(atoms, range(len(atoms)))
[all …]
/dports/science/madness/madness-ebb3fd7/src/apps/polar/
H A Dmolecule.cc223 atoms[i].x, atoms[i].y, atoms[i].z); in print()
233 return distance(atoms[i].x, atoms[i].y, atoms[i].z, in inter_atomic_distance()
234 atoms[j].x, atoms[j].y, atoms[j].z); in inter_atomic_distance()
301 xx += atoms[i].x*atoms[i].q; in center()
302 yy += atoms[i].y*atoms[i].q; in center()
350 double x=atoms[i].x, y=atoms[i].y, z=atoms[i].z; in test_for_op()
379 double r[3] = {atoms[i].x, atoms[i].y, atoms[i].z}; in swapaxes()
381 atoms[i].x=r[0]; atoms[i].y=r[1]; atoms[i].z=r[2]; in swapaxes()
468 double q = atoms[i].atomic_number, x[3] = {atoms[i].x, atoms[i].y, atoms[i].z}; in orient()
482 r[0]=atoms[i].x; r[1]=atoms[i].y, r[2]= atoms[i].z; in orient()
[all …]
/dports/science/py-ase/ase-3.22.0/ase/test/fio/
H A Dtest_aims_io.py9 atoms = bulk("Si") variable
10 atoms.positions[0, 0] -= 0.01
16 def test_cartesian(atoms=atoms): argument
18 atoms.write(file, format=format)
26 def test_scaled(atoms=atoms): argument
33 atoms.positions,
39 def test_scaled_wrapped(atoms=atoms): argument
47 atoms.positions,
51 atoms.wrap()
53 atoms.positions,
[all …]

12345678910>>...213