| /dports/science/gromacs/gromacs-2021.4/src/external/tng_io/src/compression/ |
| H A D | tng_compress.c | 107 … quant_inter[iframe*natoms*3+i*3+j]=quant[iframe*natoms*3+i*3+j]-quant[(iframe-1)*natoms*3+i*3+j]; in quant_inter_differences()
118 quant_intra[iframe*natoms*3+j]=quant[iframe*natoms*3+j]; in quant_intra_differences()
122 … quant_intra[iframe*natoms*3+i*3+j]=quant[iframe*natoms*3+i*3+j]-quant[iframe*natoms*3+(i-1)*3+j]; in quant_intra_differences()
486 length=natoms*3; in compress_quantized_vel()
1611 unquantize(posd+natoms*3,natoms,nframes-1,PRECISION(*prec_hi,*prec_lo),quant+natoms*3); in tng_compress_uncompress_pos_gen()
1613 …unquantize_float(posf+natoms*3,natoms,nframes-1,(float)PRECISION(*prec_hi,*prec_lo),quant+natoms*3… in tng_compress_uncompress_pos_gen()
1615 memcpy(posi+natoms*3,quant+natoms*3,natoms*3*(nframes-1)*sizeof *posi); in tng_compress_uncompress_pos_gen()
1625 unquantize_intra_differences_int(posi+natoms*3,natoms,nframes-1,quant+natoms*3); in tng_compress_uncompress_pos_gen()
1747 unquantize(veld+natoms*3,natoms,nframes-1,PRECISION(*prec_hi,*prec_lo),quant+natoms*3); in tng_compress_uncompress_vel_gen()
1749 …unquantize_float(velf+natoms*3,natoms,nframes-1,(float)PRECISION(*prec_hi,*prec_lo),quant+natoms*3… in tng_compress_uncompress_vel_gen()
[all …]
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| /dports/science/siesta/siesta-4.1.5/Src/ |
| H A D | dynamics.f | 106 real(dp), intent(in) :: dt,fa(3,natoms), ma(natoms),
109 $ va(3,natoms),xa(3,natoms)
1137 . va(3,natoms),vn,xa(3,natoms)
1335 xaold(1:3,1:natoms) = xa(1:3,1:natoms)
1336 xa(1:3,1:natoms) = xanew(1:3,1:natoms)
1447 . va(3,natoms),xa(3,natoms)
1616 sdot(1:3,1:natoms) = rfac * sdot(1:3,1:natoms)
1795 . dt,fa(3,natoms),kin,ma(natoms),
1796 . va(3,natoms),xa(3,natoms)
1966 . dt,fa(3,natoms),kin,ma(natoms),
[all …]
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| /dports/biology/babel/babel-1.6/ |
| H A D | tosmiles.c | 32 …ck_alloc(&blk, "iiii", &rank, frag->natoms, &primesum, frag->natoms, &tmprank, frag->natoms, &prim… in contabtosmiles()
154 for(a=0; a<natoms; a++) in sortranks()
184 for(a=0; a<natoms; a++) in resolveties()
194 for(a=0; a<natoms; a++) in resolveties()
251 natoms = frag->natoms; in generatesmilesstring()
256 …ock_alloc(&blk, "iiiB", &bracketstack, natoms, &ringstack, natoms*md_MAXBONDS, &neworder, natoms, … in generatesmilesstring()
283 while(natoms < frag->natoms && atom != -1) in generatesmilesstring()
307 if(natoms != frag->natoms-1) in generatesmilesstring()
313 natoms ++; in generatesmilesstring()
394 natoms ++; in generatesmilesstring()
[all …]
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| /dports/science/nwchem/nwchem-7b21660b82ebd85ef659f6fba7e1e73433b0bd0a/src/hessian/analytic/dft/ |
| H A D | xc_nucder_gen.F | 96 integer natoms
131 call dfill(9*natoms*natoms, 0.0d0, hess, 1)
138 do i = 1, natoms
203 call output(hess,1,3*natoms,1,3*natoms,3*natoms,3*natoms,1)
208 if (.not. MA_push_get(MT_DBL, natoms*natoms*9, 'ti_hess',
212 call dcopy(natoms*natoms*9, hess, 1, dbl_mb(k_ti_hess), 1)
286 integer natoms
287 double precision hess(3,natoms,3*natoms)
289 do i = 2, natoms
290 do j = 1, 3*natoms
[all …]
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| /dports/science/nwchem-data/nwchem-7.0.2-release/src/hessian/analytic/dft/ |
| H A D | xc_nucder_gen.F | 96 integer natoms
131 call dfill(9*natoms*natoms, 0.0d0, hess, 1)
138 do i = 1, natoms
203 call output(hess,1,3*natoms,1,3*natoms,3*natoms,3*natoms,1)
208 if (.not. MA_push_get(MT_DBL, natoms*natoms*9, 'ti_hess',
212 call dcopy(natoms*natoms*9, hess, 1, dbl_mb(k_ti_hess), 1)
286 integer natoms
287 double precision hess(3,natoms,3*natoms)
289 do i = 2, natoms
290 do j = 1, 3*natoms
[all …]
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| /dports/science/nwchem-data/nwchem-7.0.2-release/src/esp/ |
| H A D | esp_fit.F | 19 real*8 x(3,natoms),q(natoms),qf(ndim,6)
22 integer n(natoms),l(natoms)
45 do 4 j=i,natoms
66 do 7 j=1,natoms
73 do 8 i=1,natoms
82 b(natoms+1)=charge
84 ndima=natoms+1
211 do 21 i=1,natoms
234 do 26 i=1,natoms
253 do 28 i=1,natoms
[all …]
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| /dports/science/nwchem/nwchem-7b21660b82ebd85ef659f6fba7e1e73433b0bd0a/src/esp/ |
| H A D | esp_fit.F | 19 real*8 x(3,natoms),q(natoms),qf(ndim,6)
22 integer n(natoms),l(natoms)
45 do 4 j=i,natoms
66 do 7 j=1,natoms
73 do 8 i=1,natoms
82 b(natoms+1)=charge
84 ndima=natoms+1
211 do 21 i=1,natoms
234 do 26 i=1,natoms
253 do 28 i=1,natoms
[all …]
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| /dports/science/plumed/plumed2-2.7.2/src/cltools/ |
| H A D | SimpleMD.cpp | 225 for(int i=0; i<natoms; i++) { in read_positions()
364 fprintf(fp,"%d\n",natoms); in write_positions()
382 fprintf(fp,"%d\n",natoms); in write_final_positions()
474 read_natoms(inputfile,natoms); in main()
500 listsize=maxneighbour*natoms/2; in main()
503 positions.resize(natoms); in main()
504 positions0.resize(natoms); in main()
505 velocities.resize(natoms); in main()
506 forces.resize(natoms); in main()
507 masses.resize(natoms); in main()
[all …]
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| /dports/science/gromacs/gromacs-2021.4/src/gromacs/fileio/ |
| H A D | g96io.cpp | 66 nwanted = fr->natoms; in read_g96_pos()
84 natoms = 0; in read_g96_pos()
157 natoms++; in read_g96_pos()
167 fr->natoms = natoms; in read_g96_pos()
169 return natoms; in read_g96_pos()
178 nwanted = fr->natoms; in read_g96_vel()
190 natoms = 0; in read_g96_vel()
222 return natoms; in read_g96_vel()
235 natoms = 0; in read_g96_conf()
339 fr->natoms = natoms; in read_g96_conf()
[all …]
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| /dports/science/py-MDAnalysis/MDAnalysis-0.19.2/MDAnalysis/lib/formats/src/ |
| H A D | xdrfile_trr.c | 183 for (i = 0; (i < sh->natoms); i++) in do_htrn()
189 if (xdrfile_read_double(dx, sh->natoms * DIM, xd) == sh->natoms * DIM) { in do_htrn()
202 for (i = 0; (i < sh->natoms); i++) in do_htrn()
208 if (xdrfile_read_double(dx, sh->natoms * DIM, xd) == sh->natoms * DIM) { in do_htrn()
225 if (xdrfile_read_double(dx, sh->natoms * DIM, xd) == sh->natoms * DIM) { in do_htrn()
285 if (xdrfile_read_float(fx, sh->natoms * DIM, xd) == sh->natoms * DIM) { in do_htrn()
303 if (xdrfile_read_float(fx, sh->natoms * DIM, xd) == sh->natoms * DIM) { in do_htrn()
319 if (xdrfile_read_float(fx, sh->natoms * DIM, xd) == sh->natoms * DIM) { in do_htrn()
347 sh->natoms = *natoms; in do_trn()
358 *natoms = sh->natoms; in do_trn()
[all …]
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| H A D | xdrfile_xtc.c | 39 int xtc_header(XDRFILE *xd, int *natoms, int *step, float *time, in xtc_header() argument
53 if ((result = xdrfile_write_int(natoms, n, xd)) != n) in xtc_header()
73 result = xdrfile_decompress_coord_float(x[0], natoms, prec, xd); in xtc_coord()
74 if (result != *natoms) in xtc_coord()
77 result = xdrfile_compress_coord_float(x[0], *natoms, *prec, xd); in xtc_coord()
78 if (result != *natoms) in xtc_coord()
85 int read_xtc_natoms(char *fn, int *natoms) { in read_xtc_natoms() argument
93 result = xtc_header(xd, natoms, &step, &time, TRUE); in read_xtc_natoms()
105 if ((result = xtc_header(xd, &natoms, step, time, TRUE)) != exdrOK) in read_xtc()
108 if ((result = xtc_coord(xd, &natoms, box, x, prec, 1)) != exdrOK) in read_xtc()
[all …]
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| /dports/science/nwchem-data/nwchem-7.0.2-release/contrib/ |
| H A D | view_steps.pl | 46 $natoms = $1;
52 $natoms = $1;
87 print OUTPUT "$natoms\n";
127 for ($ii=1; $ii<=$natoms; $ii++) {
138 for ($ii=1; $ii<=$natoms; $ii++) {
142 $ioff_steps += $natoms;
182 $ioff = ($istep-1)*$natoms;
184 for ($ii=1; $ii<=$natoms; $ii++) {
207 $ioff = ($istep-1)*$natoms;
208 $joff = ($jstep-1)*$natoms;
[all …]
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| /dports/science/nwchem/nwchem-7b21660b82ebd85ef659f6fba7e1e73433b0bd0a/contrib/ |
| H A D | view_steps.pl | 46 $natoms = $1;
52 $natoms = $1;
87 print OUTPUT "$natoms\n";
127 for ($ii=1; $ii<=$natoms; $ii++) {
138 for ($ii=1; $ii<=$natoms; $ii++) {
142 $ioff_steps += $natoms;
182 $ioff = ($istep-1)*$natoms;
184 for ($ii=1; $ii<=$natoms; $ii++) {
207 $ioff = ($istep-1)*$natoms;
208 $joff = ($jstep-1)*$natoms;
[all …]
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| /dports/science/nwchem/nwchem-7b21660b82ebd85ef659f6fba7e1e73433b0bd0a/src/nwdft/dftgrad/ |
| H A D | j_nucder_gen.F | 82 integer natoms
114 call dfill(9*natoms*natoms, 0.0d0, hess, 1)
116 do i = 1, natoms
160 do i = 1, natoms
209 do i = 1, natoms
236 do i = 1, natoms
254 call output(hess,1,3*natoms,1,3*natoms,3*natoms,3*natoms,1)
258 if (.not. MA_push_get(MT_DBL, natoms*natoms*9, 'ti_hess',
262 call dcopy(natoms*natoms*9, hess, 1, dbl_mb(k_ti_hess), 1)
434 integer ldim, natoms
[all …]
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| /dports/science/nwchem-data/nwchem-7.0.2-release/src/nwdft/dftgrad/ |
| H A D | j_nucder_gen.F | 82 integer natoms
114 call dfill(9*natoms*natoms, 0.0d0, hess, 1)
116 do i = 1, natoms
160 do i = 1, natoms
209 do i = 1, natoms
236 do i = 1, natoms
254 call output(hess,1,3*natoms,1,3*natoms,3*natoms,3*natoms,1)
258 if (.not. MA_push_get(MT_DBL, natoms*natoms*9, 'ti_hess',
262 call dcopy(natoms*natoms*9, hess, 1, dbl_mb(k_ti_hess), 1)
434 integer ldim, natoms
[all …]
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| /dports/textproc/fox-xml/fox-4.1.2-91-g9c6716e/wcml/ |
| H A D | m_wcml_molecule.F90 | 360 do i = 1, natoms
403 do i = 1, natoms
446 natoms = size(x)
448 do i = 1, natoms
485 call addDlpolyMatrix(xf, x(:natoms), y(:natoms), z(:natoms), elements)
494 do i = 1, natoms
537 do i = 1, natoms
580 do i = 1, natoms
662 call addDlpolyMatrix(xf, x(:natoms), y(:natoms), z(:natoms), elements)
1202 call addDlpolyMatrix(xf, x(:natoms), y(:natoms), z(:natoms), elements)
[all …]
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| /dports/science/nwchem/nwchem-7b21660b82ebd85ef659f6fba7e1e73433b0bd0a/src/property/ |
| H A D | hnd_mulken.F | 89 if(.not.ma_push_get(mt_dbl,natoms*natoms,'atgross',l_atov,
147 call dcopy(natoms*natoms, 0.0d0, 0, dbl_mb(k_atov), 1)
217 do iatom = 1, natoms
232 do jatom = 1, natoms
316 if (.not.ma_push_get(mt_dbl,natoms*natoms,'b mat',l_b,k_b))
318 call dcopy(natoms*natoms, 0.0d0, 0, dbl_mb(k_b), 1)
326 do iatom = 1, natoms
351 do jatom=1,natoms
377 do iatom = 1, natoms
400 do jatom = 1, natoms
[all …]
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| /dports/science/nwchem-data/nwchem-7.0.2-release/src/property/ |
| H A D | hnd_mulken.F | 89 if(.not.ma_push_get(mt_dbl,natoms*natoms,'atgross',l_atov,
147 call dcopy(natoms*natoms, 0.0d0, 0, dbl_mb(k_atov), 1)
217 do iatom = 1, natoms
232 do jatom = 1, natoms
316 if (.not.ma_push_get(mt_dbl,natoms*natoms,'b mat',l_b,k_b))
318 call dcopy(natoms*natoms, 0.0d0, 0, dbl_mb(k_b), 1)
326 do iatom = 1, natoms
351 do jatom=1,natoms
377 do iatom = 1, natoms
400 do jatom = 1, natoms
[all …]
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| /dports/biology/molden/molden5.8/ |
| H A D | rdcor.f | 35 natoms = 0
42 natoms = itype
49 nat(natoms) = itype
85 natoms = 0
89 natoms = natoms + 1
93 nat(natoms) = itype
110 do i=1,natoms
119 do i=1,natoms
121 do j=i+1,natoms
127 natoms = natoms - 1
[all …]
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| /dports/science/gromacs/gromacs-2021.4/src/gromacs/gmxana/ |
| H A D | eigio.cpp | 49 int* natoms, in read_eigenvectors() argument
72 *natoms = head.natoms; in read_eigenvectors()
73 snew(*xav, *natoms); in read_eigenvectors()
78 snew(*xref, *natoms); in read_eigenvectors()
79 for (i = 0; i < *natoms; i++) in read_eigenvectors()
119 snew(x, *natoms); in read_eigenvectors()
139 snew((*eigvec)[*nvec], *natoms); in read_eigenvectors()
140 for (i = 0; i < *natoms; i++) in read_eigenvectors()
170 ndim = natoms * DIM; in write_eigenvectors()
172 snew(x, natoms); in write_eigenvectors()
[all …]
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| /dports/science/nwchem/nwchem-7b21660b82ebd85ef659f6fba7e1e73433b0bd0a/src/optim/string/ |
| H A D | string.F | 147 size = 3*natoms
345 & natoms,middle,
397 & natoms,middle,
716 do j=1,natoms
1067 real*8 new(3,natoms), old(3,natoms)
1100 integer natoms local
1101 real*8 new(3,natoms), old(3,natoms)
1245 integer natoms local
1283 do i=1,natoms
1927 do j=1,natoms
[all …]
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| /dports/science/nwchem-data/nwchem-7.0.2-release/src/optim/string/ |
| H A D | string.F | 147 size = 3*natoms
345 & natoms,middle,
397 & natoms,middle,
713 do j=1,natoms
1064 real*8 new(3,natoms), old(3,natoms)
1097 integer natoms local
1098 real*8 new(3,natoms), old(3,natoms)
1242 integer natoms local
1280 do i=1,natoms
1828 do j=1,natoms
[all …]
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| /dports/science/lammps/lammps-stable_29Sep2021/tools/i-pi/ipi/engine/ |
| H A D | beads.py | 73 def __init__(self, natoms, nbeads): argument
81 self.resize(natoms, nbeads)
83 def resize(self, natoms, nbeads): argument
100 self.natoms = natoms
161 newbd = Beads(self.natoms, self.nbeads)
183 m3 = np.zeros((self.nbeads,3*self.natoms),float)
184 m3[:,0:3*self.natoms:3] = self.m
185 m3[:,1:3*self.natoms:3] = m3[:,0:3*self.natoms:3]
186 m3[:,2:3*self.natoms:3] = m3[:,0:3*self.natoms:3]
263 natoms = self.natoms
[all …]
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| /dports/science/lammps/lammps-stable_29Sep2021/src/ |
| H A D | molecule.cpp | 183 for (int i = 0; i < natoms; i++) { in compute_center()
188 center[0] /= natoms; in compute_center()
189 center[1] /= natoms; in compute_center()
190 center[2] /= natoms; in compute_center()
195 for (int i = 0; i < natoms; i++) { in compute_center()
202 for (int i = 0; i < natoms; i++) { in compute_center()
389 for (int i = 0; i < natoms; i++) in compute_inertia()
506 if (natoms < 1) in read()
666 if (natoms != 1) in read()
714 for (int i = 0; i < natoms; i++) in coords()
[all …]
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| /dports/science/gromacs/gromacs-2021.4/src/gromacs/coordinateio/outputadapters/ |
| H A D | outputselector.cpp | 69 int natoms = sel.atomCount(); in adjustAtomInformation() local
71 selectionAtoms->nr = natoms; in adjustAtomInformation()
75 srenew(selectionAtoms->atom, natoms); in adjustAtomInformation()
97 for (int i = 0; i < natoms; i++) in adjustAtomInformation()
124 size_t natoms = sel_.atomCount(); in processFrame() local
126 input->natoms = natoms; in processFrame()
128 localX_.resize(natoms); in processFrame()
131 localV_.resize(natoms); in processFrame()
135 localF_.resize(natoms); in processFrame()
139 localIndex_.resize(natoms); in processFrame()
[all …]
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