| /dports/science/quantum-espresso/q-e-qe-6.7.0/dft-d3/ |
| H A D | test_code.f90 | 32 read(*,*) latvecs(1,1), latvecs(2,1), latvecs(3,1)
33 read(*,*) latvecs(1,2), latvecs(2,2), latvecs(3,2)
34 read(*,*) latvecs(1,3), latvecs(2,3), latvecs(3,3)
36 latvecs(:,:) = latvecs(:,:) * a0
40 latvecs(:,:) = latvecs(:,:) ! * 1.8897261
125 latvecs(j,i)=latvecs(j,i) + 0.0001
127 latvecs(j,i)=latvecs(j,i) - 0.0002
155 latvecs(1,1)=latvecs(1,1) + 0.0001
159 latvecs(1,1)=latvecs(1,1)-0.0001
164 latvecs(2,2)=latvecs(2,2) + 0.0001
[all …]
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| H A D | dftd3_qe.f90 | 58 subroutine dftd3_pbc_gdisp(this, coords, izp, latvecs, & argument
64 real(wp), intent(in) :: latvecs(:,:) local
82 call set_criteria(this%rthr, latvecs, rtmp3)
84 call set_criteria(this%cn_thr, latvecs, rtmp3)
91 & stress_dftd3, latvecs, rep_vdw, rep_cn, this%rthr, .false., this%cn_thr)
94 stress_dftd3(:,:) = -matmul(stress_dftd3, transpose(latvecs))&
95 & / abs(determinant(latvecs))
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| H A D | api.f90 | 230 subroutine dftd3_pbc_dispersion(this, coords, izp, latvecs, disp, grads, & argument
235 real(wp), intent(in) :: latvecs(:,:) local
261 call set_criteria(this%rthr, latvecs, rtmp3)
263 call set_criteria(this%cn_thr, latvecs, rtmp3)
267 & this%version, this%noabc, e6, e8, e10, e12, e6abc, latvecs, &
279 & stress, latvecs, rep_vdw, rep_cn, this%rthr, .false., this%cn_thr)
282 stress(:,:) = -matmul(stress, transpose(latvecs))&
283 & / abs(determinant(latvecs))
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| /dports/science/dftbplus/dftbplus-19.1/tools/dptools/src/dptools/ |
| H A D | geometry.py | 33 def __init__(self, specienames, indexes, coords, latvecs=None, origin=None, argument
55 self.periodic = latvecs is not None
57 self.latvecs = np.array(latvecs, dtype=float)
58 self._invlatvecs = la.inv(self.latvecs)
61 self.coords = np.dot(self.relcoords, self.latvecs) + self.origin
67 self.latvecs = None
72 def setlattice(self, latvecs, origin=None): argument
79 self.latvecs = np.array(latvecs, dtype=float)
80 self._invlatvecs = la.inv(self.latvecs)
108 if np.any(abs(self.latvecs - other.latvecs) > tolerance):
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| H A D | gen.py | 79 latvecs = np.empty((3, 3), dtype=float)
81 latvecs[jj] = np.array(lines[natom+3+jj].split(), dtype=float)
84 latvecs = None
85 geometry = Geometry(specienames, indexes, coords, latvecs, origin,
119 latvecs = _round_to_zero(geo.latvecs, _TOLERANCE)
120 for vec in latvecs:
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| H A D | cif.py | 32 for vv in geometry.latvecs], dtype=float)
38 v1 = geometry.latvecs[i1]
39 v2 = geometry.latvecs[i2]
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| /dports/science/dftbplus/dftbplus-19.1/tools/dptools/src/dptools/scripts/ |
| H A D | repeatgen.py | 81 latvecs = geo.latvecs
83 latvecs = np.fromfile(options.latticefile, sep=' ')
84 if len(latvecs) != 9:
88 latvecs.shape = (3, 3)
90 if latvecs is None:
94 newgeo = _repeatgeo(geo, latvecs, repeats)
102 def _repeatgeo(geo, latvecs, repeats): argument
115 shift = np.sum(latvecs * currepeats[:, np.newaxis], axis=0)
122 newlatvecs = latvecs * repeats[:, np.newaxis]
125 newgeo = Geometry(geo.specienames, allinds, allcoords, latvecs=newlatvecs,
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| H A D | straingen.py | 103 if geometry.latvecs is not None:
104 geometry.latvecs = np.dot(geometry.latvecs, strainmtx)
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| /dports/science/dftbplus/dftbplus-19.1/test/prog/dftb+/sockets/H2O/ |
| H A D | sockettools.py | 5 def frac2cart(latvecs,coords): argument
8 newcoords[iAt] = np.dot(np.transpose(latvecs),coords[iAt])
32 latvecs = np.empty((3, 3), dtype=float)
35 latvecs[ii] = [ float(s) for s in line.split() ]
37 coords = frac2cart(latvecs,coords)
40 latvecs = None
41 return specienames, species, coords, origin, latvecs
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| H A D | prerun.py | 49 specienames, species, coords, origin, latvecs = readgen("ice.gen")
51 latvecs /= a0
58 connection.sendall(latvecs)
60 connection.sendall(la.inv(latvecs))
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| /dports/science/dftbplus/dftbplus-19.1/test/prog/dftb+/sockets/H2O_cluster/ |
| H A D | sockettools.py | 5 def frac2cart(latvecs,coords): argument
8 newcoords[iAt] = np.dot(np.transpose(latvecs),coords[iAt])
32 latvecs = np.empty((3, 3), dtype=float)
35 latvecs[ii] = [ float(s) for s in line.split() ]
37 coords = frac2cart(latvecs,coords)
40 latvecs = None
41 return specienames, species, coords, origin, latvecs
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| H A D | prerun.py | 50 specienames, species, coords, origin, latvecs = readgen("geo.gen")
52 if (latvecs):
53 latvecs /= a0
56 latvecs = np.empty((3, 3), dtype=float)
64 connection.sendall(latvecs)
67 connection.sendall(la.inv(latvecs))
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| /dports/science/dftbplus/dftbplus-19.1/test/prog/dftb+/sockets/diamond_exit/ |
| H A D | sockettools.py | 5 def frac2cart(latvecs,coords): argument
8 newcoords[iAt] = np.dot(np.transpose(latvecs),coords[iAt])
32 latvecs = np.empty((3, 3), dtype=float)
35 latvecs[ii] = [ float(s) for s in line.split() ]
37 coords = frac2cart(latvecs,coords)
40 latvecs = None
41 return specienames, species, coords, origin, latvecs
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| H A D | prerun.py | 35 specienames, species, coords, origin, latvecs = readgen("diamond.gen")
37 latvecs /= a0
44 connection.sendall(latvecs)
46 connection.sendall(la.inv(latvecs))
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| /dports/science/dftbplus/dftbplus-19.1/test/prog/dftb+/sockets/ |
| H A D | sockettools.py | 5 def frac2cart(latvecs,coords): argument
8 newcoords[iAt] = np.dot(np.transpose(latvecs),coords[iAt])
32 latvecs = np.empty((3, 3), dtype=float)
35 latvecs[ii] = [ float(s) for s in line.split() ]
37 coords = frac2cart(latvecs,coords)
40 latvecs = None
41 return specienames, species, coords, origin, latvecs
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| /dports/science/dftbplus/dftbplus-19.1/test/prog/dftb+/sockets/diamond/ |
| H A D | sockettools.py | 5 def frac2cart(latvecs,coords): argument
8 newcoords[iAt] = np.dot(np.transpose(latvecs),coords[iAt])
32 latvecs = np.empty((3, 3), dtype=float)
35 latvecs[ii] = [ float(s) for s in line.split() ]
37 coords = frac2cart(latvecs,coords)
40 latvecs = None
41 return specienames, species, coords, origin, latvecs
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| H A D | prerun.py | 35 specienames, species, coords, origin, latvecs = readgen("diamond.gen")
37 latvecs /= a0
44 connection.sendall(latvecs)
46 connection.sendall(la.inv(latvecs))
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| /dports/science/octopus/octopus-10.5/external_libs/dftd3/ |
| H A D | api.f90 | 225 subroutine dftd3_pbc_dispersion(this, coords, izp, latvecs, disp, grads, & argument
230 real(wp), intent(in) :: latvecs(:,:) local
256 call set_criteria(this%rthr, latvecs, rtmp3)
258 call set_criteria(this%cn_thr, latvecs, rtmp3)
262 & this%version, this%noabc, e6, e8, e10, e12, e6abc, latvecs, &
274 & stress, latvecs, rep_vdw, rep_cn, this%rthr, .false., this%cn_thr)
277 stress(1:3, 1:3) = -matmul(stress(1:3, 1:3), transpose(latvecs(1:3, 1:3)))&
278 & / abs(determinant(latvecs))
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| /dports/science/dftbplus/dftbplus-19.1/external/dftd3/origin/lib/ |
| H A D | api.f90 | 222 subroutine dftd3_pbc_dispersion(this, coords, izp, latvecs, disp, grads, & argument
227 real(wp), intent(in) :: latvecs(:,:) local
251 call set_criteria(this%rthr, latvecs, rtmp3)
253 call set_criteria(this%cn_thr, latvecs, rtmp3)
257 & this%version, this%noabc, e6, e8, e10, e12, e6abc, latvecs, &
269 & stress, latvecs, rep_vdw, rep_cn, this%rthr, .false., this%cn_thr)
272 stress(:,:) = -matmul(stress, transpose(latvecs))&
273 & / abs(determinant(latvecs))
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| /dports/science/dftbplus/dftbplus-19.1/tools/dptools/bin/ |
| H A D | xyz2gen | 48 latvecs = tmp.reshape((3, 3))
50 geo.setlattice(latvecs)
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| /dports/science/qwalk/mainline-1.0.1-300-g1b7e381/utils/autogen/ |
| H A D | crystal2qmc.py | 315 latvecs = lat_parm['latvecs']
317 cross01 = np.cross(latvecs[0], latvecs[1])
318 cross12 = np.cross(latvecs[1], latvecs[2])
319 cross02 = np.cross(latvecs[0], latvecs[2])
322 heights[0]=abs(np.dot(latvecs[0], cross12)/np.dot(cross12,cross12)**.5)
323 heights[1]=abs(np.dot(latvecs[1], cross02)/np.dot(cross02,cross02)**.5)
324 heights[2]=abs(np.dot(latvecs[2], cross01)/np.dot(cross01,cross01)**.5)
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| /dports/science/quantum-espresso/q-e-qe-6.7.0/PW/src/ |
| H A D | stress.f90 | 58 REAL(DP) :: latvecs(3,3) local
124 latvecs(:,:) = at(:,:)*alat
127 CALL dftd3_pbc_gdisp( dftd3, tau, atnum, latvecs, &
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| /dports/science/dftbplus/dftbplus-19.1/prog/dftb+/lib_dftb/ |
| H A D | periodic.F90 | 1056 subroutine fractionalCartesian(cartCoords,latvecs) argument
1062 real(dp), intent(in) :: latvecs(3,3) local
1066 cartCoords = matmul(latvecs,cartCoords)
1072 subroutine cartesianFractional(cartCoords,latvecs) argument
1078 real(dp), intent(in) :: latvecs(3,3) local
1084 call invert33(invLatVecs, latvecs)
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| /dports/science/dftbplus/dftbplus-19.1/api/mm/ |
| H A D | dftbplus.h | 177 const double *latvecs);
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| /dports/science/plumed/plumed2-2.7.2/patches/qespresso-6.2.diff/PW/src/ |
| H A D | forces.f90 | 87 REAL(DP) :: latvecs(3,3) local
145 latvecs(:,:) = at(:,:)*alat
148 call dftd3_pbc_gdisp(dftd3, tau, atnum, latvecs, &
|