Home
last modified time | relevance | path

Searched refs:nstates (Results 1 – 25 of 1294) sorted by relevance

12345678910>>...52

/dports/biology/bcftools/bcftools-1.14/
H A DHMM.c131 hmm->nstates = nstates; in hmm_init()
132 hmm->curr_tprob = (double*) malloc(sizeof(double)*nstates*nstates); in hmm_init()
133 hmm->tmp = (double*) malloc(sizeof(double)*nstates*nstates); in hmm_init()
142 if ( snapshot && snapshot->nstates!=hmm->nstates ) in hmm_snapshot()
156 snapshot->nstates = hmm->nstates; in hmm_snapshot()
201 …ltiply_matrix(hmm->nstates, hmm->tprob_arr, hmm->tprob_arr+(i-1)*hmm->nstates*hmm->nstates, hmm->t… in hmm_set_tprob()
217 …(hmm->curr_tprob, hmm->tprob_arr+n*hmm->nstates*hmm->nstates, sizeof(*hmm->curr_tprob)*hmm->nstate… in _set_tprob()
242 int i,j, nstates = hmm->nstates; in hmm_run_viterbi() local
286 assert( iptr<nstates && hmm->vpath[i*nstates + iptr]<nstates ); in hmm_run_viterbi()
307 int i,j,k, nstates = hmm->nstates; in hmm_run_fwd_bwd() local
[all …]
/dports/biology/bio-mocha/bcftools-1.14/
H A DHMM.c131 hmm->nstates = nstates; in hmm_init()
132 hmm->curr_tprob = (double*) malloc(sizeof(double)*nstates*nstates); in hmm_init()
133 hmm->tmp = (double*) malloc(sizeof(double)*nstates*nstates); in hmm_init()
142 if ( snapshot && snapshot->nstates!=hmm->nstates ) in hmm_snapshot()
156 snapshot->nstates = hmm->nstates; in hmm_snapshot()
201 …ltiply_matrix(hmm->nstates, hmm->tprob_arr, hmm->tprob_arr+(i-1)*hmm->nstates*hmm->nstates, hmm->t… in hmm_set_tprob()
217 …(hmm->curr_tprob, hmm->tprob_arr+n*hmm->nstates*hmm->nstates, sizeof(*hmm->curr_tprob)*hmm->nstate… in _set_tprob()
242 int i,j, nstates = hmm->nstates; in hmm_run_viterbi() local
286 assert( iptr<nstates && hmm->vpath[i*nstates + iptr]<nstates ); in hmm_run_viterbi()
307 int i,j,k, nstates = hmm->nstates; in hmm_run_fwd_bwd() local
[all …]
/dports/biology/py-pysam/pysam-0.18.0/bcftools/
H A DHMM.c131 hmm->nstates = nstates; in hmm_init()
132 hmm->curr_tprob = (double*) malloc(sizeof(double)*nstates*nstates); in hmm_init()
133 hmm->tmp = (double*) malloc(sizeof(double)*nstates*nstates); in hmm_init()
142 if ( snapshot && snapshot->nstates!=hmm->nstates ) in hmm_snapshot()
156 snapshot->nstates = hmm->nstates; in hmm_snapshot()
201 …ltiply_matrix(hmm->nstates, hmm->tprob_arr, hmm->tprob_arr+(i-1)*hmm->nstates*hmm->nstates, hmm->t… in hmm_set_tprob()
217 …(hmm->curr_tprob, hmm->tprob_arr+n*hmm->nstates*hmm->nstates, sizeof(*hmm->curr_tprob)*hmm->nstate… in _set_tprob()
242 int i,j, nstates = hmm->nstates; in hmm_run_viterbi() local
286 assert( iptr<nstates && hmm->vpath[i*nstates + iptr]<nstates ); in hmm_run_viterbi()
307 int i,j,k, nstates = hmm->nstates; in hmm_run_fwd_bwd() local
[all …]
H A DHMM.c.pysam.c133 hmm->nstates = nstates; in hmm_init()
134 hmm->curr_tprob = (double*) malloc(sizeof(double)*nstates*nstates); in hmm_init()
135 hmm->tmp = (double*) malloc(sizeof(double)*nstates*nstates); in hmm_init()
144 if ( snapshot && snapshot->nstates!=hmm->nstates ) in hmm_snapshot()
158 snapshot->nstates = hmm->nstates; in hmm_snapshot()
203 …ltiply_matrix(hmm->nstates, hmm->tprob_arr, hmm->tprob_arr+(i-1)*hmm->nstates*hmm->nstates, hmm->t… in hmm_set_tprob()
219 …(hmm->curr_tprob, hmm->tprob_arr+n*hmm->nstates*hmm->nstates, sizeof(*hmm->curr_tprob)*hmm->nstate… in _set_tprob()
244 int i,j, nstates = hmm->nstates; in hmm_run_viterbi() local
288 assert( iptr<nstates && hmm->vpath[i*nstates + iptr]<nstates ); in hmm_run_viterbi()
309 int i,j,k, nstates = hmm->nstates; in hmm_run_fwd_bwd() local
[all …]
/dports/biology/iqtree/IQ-TREE-2.0.6/tree/
H A Dphylotreesse.cpp380 double *inv_evec = &model->getInverseEigenvectors()[ptn*nstates*nstates]; in computeTipPartialLikelihood()
512 double *this_tip_partial_lh = &tip_partial_lh[(state+nstates)*nstates]; in computeTipPartialLikelihood()
535 double *inv_evec = &all_inv_evec[m*nstates*nstates]; in computeTipPartialLikelihood()
537 this_tip_partial_lh[m*nstates + i] = inv_evec[i*nstates+state]; in computeTipPartialLikelihood()
544 double *inv_evec = &all_inv_evec[m*nstates*nstates]; in computeTipPartialLikelihood()
560 double *inv_evec = &all_inv_evec[m*nstates*nstates]; in computeTipPartialLikelihood()
577 double *inv_evec = &all_inv_evec[m*nstates*nstates]; in computeTipPartialLikelihood()
600 double *this_tip_partial_lh = &tip_partial_lh[(state+nstates)*nstates*nmixtures]; in computeTipPartialLikelihood()
603 double *inv_evec = &all_inv_evec[m*nstates*nstates]; in computeTipPartialLikelihood()
1821 size_t nstatesqr = nstates*nstates; in computeAncestralLikelihood()
[all …]
H A Dphylokernelsitemodel.cpp24 size_t nstates = aln->num_states; in computeSitemodelPartialLikelihoodEigen() local
29 size_t block = nstates * ncat; in computeSitemodelPartialLikelihoodEigen()
178 … memcpy(&partial_lh[c*nstates], &tip_partial_lh[ptn*nstates], nstates*sizeof(double)); in computeSitemodelPartialLikelihoodEigen()
219 double partial_lh_tmp[nstates]; in computeSitemodelPartialLikelihoodEigen()
327 memcpy(&partial_lh[c*nstates], &tip_partial_lh[ptn*nstates], nstates*sizeof(double)); in computeSitemodelPartialLikelihoodEigen()
412 memcpy(&partial_lh[c*nstates], &tip_partial_lh[ptn*nstates], nstates*sizeof(double)); in computeSitemodelPartialLikelihoodEigen()
540 theta += nstates; in computeSitemodelLikelihoodDervEigen()
618 partial_lh_dad += nstates; in computeSitemodelLikelihoodBranchEigen()
647 partial_lh_node += nstates; in computeSitemodelLikelihoodBranchEigen()
648 partial_lh_dad += nstates; in computeSitemodelLikelihoodBranchEigen()
[all …]
H A Dphylokernelnonrev.cpp30 size_t nstates = aln->num_states; in computeNonrevPartialLikelihood() local
48 size_t block = nstates * ncat; in computeNonrevPartialLikelihood()
168 …memcpy(&partial_lh_all[c*nstates], &tip_partial_lh[aln->STATE_UNKNOWN*nstates], nstates*sizeof(dou… in computeNonrevPartialLikelihood()
259 for (x = 0; x < nstates; x++) { in computeNonrevPartialLikelihood()
267 vleft += nstates; in computeNonrevPartialLikelihood()
275 …memcpy(&partial_lh[c*nstates], &tip_partial_lh[aln->STATE_UNKNOWN*nstates], nstates*sizeof(double)… in computeNonrevPartialLikelihood()
319 for (x = 0; x < nstates; x++) { in computeNonrevPartialLikelihood()
338 …memcpy(&partial_lh[c*nstates], &tip_partial_lh[aln->STATE_UNKNOWN*nstates], nstates*sizeof(double)… in computeNonrevPartialLikelihood()
394 size_t nstatesqr = nstates*nstates; in computeNonrevLikelihoodDerv()
397 size_t block = ncat * nstates; in computeNonrevLikelihoodDerv()
[all …]
H A Dphylokernelmixrate.h55 const size_t nstatesqr=nstates*nstates; in computeMixratePartialLikelihoodEigenSIMD()
98 VectorClass *vc_inv_evec = aligned_alloc<VectorClass>(ncat*nstates*nstates/VCSIZE); in computeMixratePartialLikelihoodEigenSIMD()
104 vc_inv_evec[(c*nstates+i)*nstates/VCSIZE+x].load_a(&inv_evec[c*nstatesqr+i*nstates+x*VCSIZE]); in computeMixratePartialLikelihoodEigenSIMD()
151 size_t addr = (c*nstates+x)*nstates/VCSIZE; in computeMixratePartialLikelihoodEigenSIMD()
172 size_t addr = (c*nstates+x)*nstates/VCSIZE; in computeMixratePartialLikelihoodEigenSIMD()
234 lh_left += nstates; in computeMixratePartialLikelihoodEigenSIMD()
235 lh_right += nstates; in computeMixratePartialLikelihoodEigenSIMD()
236 partial_lh += nstates; in computeMixratePartialLikelihoodEigenSIMD()
263 size_t addr = (c*nstates+x)*nstates/VCSIZE; in computeMixratePartialLikelihoodEigenSIMD()
338 lh_left += nstates; in computeMixratePartialLikelihoodEigenSIMD()
[all …]
H A Dphylokernelsafe.h108 ASSERT(nstates == aln->num_states && nstates >= VCSIZE && VCSIZE == VectorClass().size()); in computePartialLikelihoodEigenSIMD()
110 const size_t nstatesqr=nstates*nstates; in computePartialLikelihoodEigenSIMD()
384 lh_left += nstates; in computePartialLikelihoodEigenSIMD()
385 lh_right += nstates; in computePartialLikelihoodEigenSIMD()
386 partial_lh += nstates; in computePartialLikelihoodEigenSIMD()
474 lh_left += nstates; in computePartialLikelihoodEigenSIMD()
476 partial_lh += nstates; in computePartialLikelihoodEigenSIMD()
486 VectorClass vc_lh_left[nstates/VCSIZE], vc_lh_right[nstates/VCSIZE]; in computePartialLikelihoodEigenSIMD()
551 partial_lh += nstates; in computePartialLikelihoodEigenSIMD()
1637 switch (nstates) { in computePartialParsimonyFastSIMD()
[all …]
H A Dphylokernelnonrev.h47 size_t nstates = aln->num_states; local
63 size_t block = nstates * ncat_mix;
343 for (x = 0; x < nstates; x++) {
354 lh_left += nstates;
355 partial_lh += nstates;
403 for (x = 0; x < nstates; x++) {
431 vleft += nstates;
487 for (x = 0; x < nstates; x++) {
578 size_t nstates = aln->num_states; local
580 size_t nstatesqr = nstates*nstates;
[all …]
H A Dphylokernelmixture.h53 const size_t nstatesqr=nstates*nstates; in computeMixturePartialLikelihoodEigenSIMD()
236 res[j] = vc_partial_lh_tmp[0] * vc_inv_evec[(m*nstates+i+j)*nstates/VCSIZE]; in computeMixturePartialLikelihoodEigenSIMD()
244 lh_left += nstates; in computeMixturePartialLikelihoodEigenSIMD()
245 lh_right += nstates; in computeMixturePartialLikelihoodEigenSIMD()
246 partial_lh += nstates; in computeMixturePartialLikelihoodEigenSIMD()
340 res[j] = vc_partial_lh_tmp[0] * vc_inv_evec[(m*nstates+i+j)*nstates/VCSIZE]; in computeMixturePartialLikelihoodEigenSIMD()
351 lh_left += nstates; in computeMixturePartialLikelihoodEigenSIMD()
353 partial_lh += nstates; in computeMixturePartialLikelihoodEigenSIMD()
382 VectorClass vc_lh_left[nstates/VCSIZE], vc_lh_right[nstates/VCSIZE]; in computeMixturePartialLikelihoodEigenSIMD()
423 res[j] = vc_partial_lh_tmp[0] * vc_inv_evec[(m*nstates+i+j)*nstates/VCSIZE]; in computeMixturePartialLikelihoodEigenSIMD()
[all …]
H A Dphylokernelnew.h642 if (nstates % 2 == 0) { in dotProductTriple()
816 size_t ncat_mix, size_t nstates) in scaleLikelihood()
894 size_t nstatesqr = nstates*nstates; in computePartialInfo()
964 echild += block*nstates; in computePartialInfo()
1019 echild += block*nstates; in computePartialInfo()
1024 double expchild[nstates]; in computePartialInfo()
1068 echild += block*nstates; in computePartialInfo()
1270 const size_t states_square = nstates*nstates; in computePartialLikelihoodSIMD()
2062 theta += nstates; in computeLikelihoodBufferSIMD()
3219 theta += nstates; in computeLikelihoodFromBufferSIMD()
[all …]
/dports/science/nwchem/nwchem-7b21660b82ebd85ef659f6fba7e1e73433b0bd0a/src/qmd/
H A Dqmd_elec_prop.F23 double complex zden(nstates,nstates)
26 double precision coup1(nstates,nstates)
27 double precision coup2(nstates,nstates)
201 double precision coup1(nstates,nstates)
202 double precision coup2(nstates,nstates)
205 double complex zden(nstates,nstates)
206 double complex zham(nstates,nstates)
207 double complex ztden1(nstates,nstates)
208 double complex ztden2(nstates,nstates)
209 double complex zrk4s(nstates,nstates)
[all …]
H A Dqmd_namd_init.F7 & k_sv,state,state_p,nstates,dt_elec,
35 integer nstates ! number of states
80 if (.not.rtdb_get(rtdb,'qmd:nstates',mt_int,1,nstates))
96 write(LuOut,120) "Number of states:", nstates
119 if (.not.ma_push_get(mt_int,nstates,'swap occ',l_so,k_so))
121 if (.not.ma_push_get(mt_int,nstates,'swap vir',l_sv,k_sv))
128 if (nroots.lt.(nstates-1))
150 if (.not.ma_push_get(mt_dbl,nstates**2,'coup_p',l_coup_p,
155 if (.not.ma_push_get(mt_dbl,nstates,'energies',l_en,k_en))
193 call qmd_set_den(nstates,state,dcpl_mb(k_zden))
[all …]
H A Dqmd_tdks_enmo.F16 integer nstates local
20 integer swap_occ(nstates)
21 integer swap_vir(nstates)
24 double precision en(nstates)
82 integer nstates local
83 integer swap_occ(nstates)
84 integer swap_vir(nstates)
187 integer nstates local
188 integer swap_occ(nstates)
235 do i=1,nstates-1
[all …]
/dports/science/nwchem-data/nwchem-7.0.2-release/src/qmd/
H A Dqmd_elec_prop.F23 double complex zden(nstates,nstates)
26 double precision coup1(nstates,nstates)
27 double precision coup2(nstates,nstates)
201 double precision coup1(nstates,nstates)
202 double precision coup2(nstates,nstates)
205 double complex zden(nstates,nstates)
206 double complex zham(nstates,nstates)
207 double complex ztden1(nstates,nstates)
208 double complex ztden2(nstates,nstates)
209 double complex zrk4s(nstates,nstates)
[all …]
H A Dqmd_namd_init.F7 & k_sv,state,state_p,nstates,dt_elec,
35 integer nstates ! number of states
80 if (.not.rtdb_get(rtdb,'qmd:nstates',mt_int,1,nstates))
96 write(LuOut,120) "Number of states:", nstates
119 if (.not.ma_push_get(mt_int,nstates,'swap occ',l_so,k_so))
121 if (.not.ma_push_get(mt_int,nstates,'swap vir',l_sv,k_sv))
128 if (nroots.lt.(nstates-1))
150 if (.not.ma_push_get(mt_dbl,nstates**2,'coup_p',l_coup_p,
155 if (.not.ma_push_get(mt_dbl,nstates,'energies',l_en,k_en))
193 call qmd_set_den(nstates,state,dcpl_mb(k_zden))
[all …]
H A Dqmd_tdks_enmo.F16 integer nstates
20 integer swap_occ(nstates)
21 integer swap_vir(nstates)
24 double precision en(nstates)
82 integer nstates
83 integer swap_occ(nstates)
84 integer swap_vir(nstates)
187 integer nstates
188 integer swap_occ(nstates)
235 do i=1,nstates-1
[all …]
/dports/science/bagel/bagel-1.2.2/src/asd/
H A Dasd_base.cc167 auto out = make_shared<Matrix>(A.nstates()*B.nstates(), Ap.nstates()*Bp.nstates()); in compute_offdiagonal_1e()
231 auto out = make_shared<Matrix>(A.nstates()*B.nstates(), Ap.nstates()*Bp.nstates()); in compute_inter_2e()
232 …indices<0,2,1,3,0,1,1,1>(tmp.data(), out->data(), A.nstates(), Ap.nstates(), B.nstates(), Bp.nstat… in compute_inter_2e()
239 Matrix tmp(A.nstates()*Ap.nstates(), B.nstates()*Bp.nstates()); in compute_aET()
274 auto out = make_shared<Matrix>(A.nstates()*B.nstates(), Ap.nstates()*Bp.nstates()); in compute_aET()
288 Matrix tmp(A.nstates()*Ap.nstates(), B.nstates()*Bp.nstates()); in compute_bET()
324 auto out = make_shared<Matrix>(A.nstates()*B.nstates(), Ap.nstates()*Bp.nstates()); in compute_bET()
349 auto out = make_shared<Matrix>(A.nstates()*B.nstates(), Ap.nstates()*Bp.nstates()); in compute_abFlip()
367 auto out = make_shared<Matrix>(A.nstates()*B.nstates(), Ap.nstates()*Bp.nstates()); in compute_abET()
384 auto out = make_shared<Matrix>(A.nstates()*B.nstates(), Ap.nstates()*Bp.nstates()); in compute_aaET()
[all …]
/dports/science/quantum-espresso/q-e-qe-6.7.0/GWW/head/
H A Dlanczos_k.f9057 allocate(psi_1(npwx,nstates),psi_2(npwx,nstates),psi_3(npwx,nstates))
58 allocate(u_0(npwx,nstates),u_1(npwx,nstates))
59 allocate(alpha(nstates),beta(nstates),gamma(nstates),n_1(nstates),delta(nstates))
67 psi_1(1:npw,1:nstates)=in_states(1:npw,1:nstates)
70 do is=1,nstates
77 do is=1,nstates
106 do is=1,nstates
119 do is=1,nstates
130 do is=1,nstates
135 do is=1,nstates
[all …]
/dports/net/mpich2/mpich2-1.5/src/mpe2/src/unused/src/
H A Dstates.c32 int *nstates;
53 &(stateDefs[*nstates].start), &(stateDefs[*nstates].end),
57 stateDefs[*nstates].start, stateDefs[*nstates].end );
59 (*nstates)++;
84 while (i < nstates &&
86 if (i==nstates) {
181 int nstates;
190 if (!nstates) {
195 for (i=0; i<nstates; i++) {
227 int nstates;
[all …]
/dports/science/bagel/bagel-1.2.2/src/asd/dmrg/
H A Ddmrg_block.cc81 …const int nstates = accumulate(p.second.begin(), p.second.end(), 0, [] (int x, DMRG::BlockPair bp)… in DMRG_Block2() local
104 auto out = make_shared<Matrix>(binfo.nstates, binfo.nstates); in spin()
109 Matrix eye(source.right.nstates, source.right.nstates); in spin()
116 Matrix eye(source.left.nstates, source.left.nstates); in spin()
124 for (int i = 0; i < source.nstates(); ++i) in spin()
172 auto out = make_shared<Matrix>(target_info.nstates, source_info.nstates); in spin_lower()
185 Matrix eyeR(source.right.nstates, source.right.nstates); eyeR.unit(); in spin_lower()
199 Matrix eyeL(source.left.nstates, source.left.nstates); eyeL.unit(); in spin_lower()
216 auto out = make_shared<Matrix>(target_info.nstates, source_info.nstates); in spin_raise()
229 Matrix eyeR(source.right.nstates, source.right.nstates); eyeR.unit(); in spin_raise()
[all …]
/dports/science/dynare/dynare-4.6.4/contrib/ms-sbvar/switch_dw/switching/
H A Ddw_dirichlet_restrictions.c70 if ((nstates <= 0)) in CreateDirichletRestrictions()
104 restrictions->nstates=nstates; in CreateDirichletRestrictions()
188 NonZeroIndex=dw_CreateRectangularArray_int(nstates,nstates); in CreateMarkovStateVariable_Mixture()
192 MQ=InitializeMatrix(CreateMatrix(nstates,nstates),1.0); in CreateMarkovStateVariable_Mixture()
194 DirichletDim[0]=nstates; in CreateMarkovStateVariable_Mixture()
210 NonZeroIndex=dw_CreateRectangularArray_int(nstates,nstates); in CreateMarkovStateVariable_NoRestrictions()
214 InitializeMatrix(MQ=CreateMatrix(nstates,nstates),1.0); in CreateMarkovStateVariable_NoRestrictions()
216 for (i=nstates-1; i >= 0; i--) DirichletDim[i]=nstates; in CreateMarkovStateVariable_NoRestrictions()
233 MQ=InitializeMatrix(CreateMatrix(nstates,nstates),0.0); in CreateMarkovStateVariable_Exclusion()
262 InitializeMatrix(MQ=CreateMatrix(nstates,nstates),0.0); in CreateMarkovStateVariable_SimpleRestrictions()
[all …]
/dports/archivers/lzfse/lzfse-4591228/src/
H A Dlzfse_fse.c31 void fse_init_encoder_table(int nstates, int nsymbols, in fse_init_encoder_table() argument
35 int n_clz = __builtin_clz(nstates); in fse_init_encoder_table()
42 t[i].s0 = (int16_t)((f << k) - nstates); in fse_init_encoder_table()
57 int fse_init_decoder_table(int nstates, int nsymbols, in fse_init_decoder_table() argument
62 int n_clz = __builtin_clz(nstates); in fse_init_decoder_table()
71 if (sum_of_freq > nstates) { in fse_init_decoder_table()
77 int j0 = ((2 * nstates) >> k) - f; in fse_init_decoder_table()
86 e.delta = (int16_t)(((f + j) << k) - nstates); in fse_init_decoder_table()
117 int n_clz = __builtin_clz(nstates); in fse_init_value_decoder_table()
125 int j0 = ((2 * nstates) >> k) - f; in fse_init_value_decoder_table()
[all …]
/dports/devel/xelfviewer/XELFViewer-0.03/XArchive/3rdparty/lzfse/src/
H A Dlzfse_fse.c31 void fse_init_encoder_table(int nstates, int nsymbols, in fse_init_encoder_table() argument
35 int n_clz = __builtin_clz(nstates); in fse_init_encoder_table()
42 t[i].s0 = (int16_t)((f << k) - nstates); in fse_init_encoder_table()
57 int fse_init_decoder_table(int nstates, int nsymbols, in fse_init_decoder_table() argument
62 int n_clz = __builtin_clz(nstates); in fse_init_decoder_table()
71 if (sum_of_freq > nstates) { in fse_init_decoder_table()
77 int j0 = ((2 * nstates) >> k) - f; in fse_init_decoder_table()
86 e.delta = (int16_t)(((f + j) << k) - nstates); in fse_init_decoder_table()
117 int n_clz = __builtin_clz(nstates); in fse_init_value_decoder_table()
125 int j0 = ((2 * nstates) >> k) - f; in fse_init_value_decoder_table()
[all …]

12345678910>>...52