Home
last modified time | relevance | path

Searched refs:mocc (Results 1 – 25 of 46) sorted by relevance

12

/dports/biology/infernal/infernal-1.1.3/hmmer/src/
H A Dmodelstats.c166 float *mocc = NULL; in p7_MeanPositionRelativeEntropy() local
171 ESL_ALLOC(mocc, sizeof(float) * (hmm->M+1)); in p7_MeanPositionRelativeEntropy()
172 if ((status = p7_hmm_CalculateOccupancy(hmm, mocc, NULL)) != eslOK) goto ERROR; in p7_MeanPositionRelativeEntropy()
176 mre += mocc[k] * esl_vec_FRelEntropy(hmm->mat[k], bg->f, hmm->abc->K); in p7_MeanPositionRelativeEntropy()
177 mre /= esl_vec_FSum(mocc+1, hmm->M); in p7_MeanPositionRelativeEntropy()
183 xm = mocc[k-1]*hmm->t[k-1][p7H_MM] * log(hmm->t[k-1][p7H_MM] / bg->p1); in p7_MeanPositionRelativeEntropy()
184 …xi = mocc[k-1]*hmm->t[k-1][p7H_MI] * (log(hmm->t[k-1][p7H_MM] / bg->p1) + log(hmm->t[k-1][p7H_IM] … in p7_MeanPositionRelativeEntropy()
185 xd = (1.-mocc[k-1])*hmm->t[k-1][p7H_DM] * log(hmm->t[k-1][p7H_DM] / bg->p1); in p7_MeanPositionRelativeEntropy()
188 tre /= esl_vec_FSum(mocc+2, hmm->M-1); in p7_MeanPositionRelativeEntropy()
190 free(mocc); in p7_MeanPositionRelativeEntropy()
[all …]
H A Dp7_hmm.c627 float *mocc = NULL; in p7_hmm_SetComposition() local
632 ESL_ALLOC(mocc, sizeof(float) * (hmm->M+1)); in p7_hmm_SetComposition()
635 p7_hmm_CalculateOccupancy(hmm, mocc, iocc); in p7_hmm_SetComposition()
640 esl_vec_FAddScaled(hmm->compo, hmm->mat[k], mocc[k], hmm->abc->K); in p7_hmm_SetComposition()
647 free(mocc); in p7_hmm_SetComposition()
652 if (mocc != NULL) free(mocc); in p7_hmm_SetComposition()
1338 p7_hmm_CalculateOccupancy(const P7_HMM *hmm, float *mocc, float *iocc) in p7_hmm_CalculateOccupancy() argument
1342 mocc[0] = 0.; /* no M_0 state */ in p7_hmm_CalculateOccupancy()
1345 mocc[k] = mocc[k-1] * (hmm->t[k-1][p7H_MM] + hmm->t[k-1][p7H_MI]) + in p7_hmm_CalculateOccupancy()
1346 (1.0-mocc[k-1]) * hmm->t[k-1][p7H_DM]; in p7_hmm_CalculateOccupancy()
[all …]
H A Dp7_domaindef.c79 ddef->mocc = ddef->btot = ddef->etot = NULL; in p7_domaindef_Create()
86 ESL_ALLOC(ddef->mocc, sizeof(float) * (Lalloc+1)); in p7_domaindef_Create()
90 ddef->mocc[0] = ddef->etot[0] = ddef->btot[0] = 0.; in p7_domaindef_Create()
156 ESL_RALLOC(ddef->mocc, p, sizeof(float) * (L+1)); in p7_domaindef_GrowTo()
256 fprintf(ofp, "%d %f\n", i, ddef->mocc[i]); in p7_domaindef_DumpPosteriors()
288 if (ddef->mocc != NULL) free(ddef->mocc); in p7_domaindef_Destroy()
414 if (ddef->mocc[j] - (ddef->btot[j] - ddef->btot[j-1]) < ddef->rt2) i = j; in p7_domaindef_ByPosteriorHeuristics()
416 if (ddef->mocc[j] >= ddef->rt1) triggered = TRUE; in p7_domaindef_ByPosteriorHeuristics()
418 else if (ddef->mocc[j] - (ddef->etot[j] - ddef->etot[j-1]) < ddef->rt2) in p7_domaindef_ByPosteriorHeuristics()
/dports/biology/hmmer/hmmer-3.3/src/
H A Dmodelstats.c166 float *mocc = NULL; in p7_MeanPositionRelativeEntropy() local
171 ESL_ALLOC(mocc, sizeof(float) * (hmm->M+1)); in p7_MeanPositionRelativeEntropy()
172 if ((status = p7_hmm_CalculateOccupancy(hmm, mocc, NULL)) != eslOK) goto ERROR; in p7_MeanPositionRelativeEntropy()
176 mre += mocc[k] * esl_vec_FRelEntropy(hmm->mat[k], bg->f, hmm->abc->K); in p7_MeanPositionRelativeEntropy()
177 mre /= esl_vec_FSum(mocc+1, hmm->M); in p7_MeanPositionRelativeEntropy()
183 xm = mocc[k-1]*hmm->t[k-1][p7H_MM] * log(hmm->t[k-1][p7H_MM] / bg->p1); in p7_MeanPositionRelativeEntropy()
184 …xi = mocc[k-1]*hmm->t[k-1][p7H_MI] * (log(hmm->t[k-1][p7H_MM] / bg->p1) + log(hmm->t[k-1][p7H_IM] … in p7_MeanPositionRelativeEntropy()
185 xd = (1.-mocc[k-1])*hmm->t[k-1][p7H_DM] * log(hmm->t[k-1][p7H_DM] / bg->p1); in p7_MeanPositionRelativeEntropy()
188 tre /= esl_vec_FSum(mocc+2, hmm->M-1); in p7_MeanPositionRelativeEntropy()
190 free(mocc); in p7_MeanPositionRelativeEntropy()
[all …]
H A Dp7_hmm.c627 float *mocc = NULL; in p7_hmm_SetComposition() local
632 ESL_ALLOC(mocc, sizeof(float) * (hmm->M+1)); in p7_hmm_SetComposition()
635 p7_hmm_CalculateOccupancy(hmm, mocc, iocc); in p7_hmm_SetComposition()
640 esl_vec_FAddScaled(hmm->compo, hmm->mat[k], mocc[k], hmm->abc->K); in p7_hmm_SetComposition()
647 free(mocc); in p7_hmm_SetComposition()
652 if (mocc != NULL) free(mocc); in p7_hmm_SetComposition()
1338 p7_hmm_CalculateOccupancy(const P7_HMM *hmm, float *mocc, float *iocc) in p7_hmm_CalculateOccupancy() argument
1342 mocc[0] = 0.; /* no M_0 state */ in p7_hmm_CalculateOccupancy()
1345 mocc[k] = mocc[k-1] * (hmm->t[k-1][p7H_MM] + hmm->t[k-1][p7H_MI]) + in p7_hmm_CalculateOccupancy()
1346 (1.0-mocc[k-1]) * hmm->t[k-1][p7H_DM]; in p7_hmm_CalculateOccupancy()
[all …]
H A Dp7_domaindef.c79 ddef->mocc = ddef->btot = ddef->etot = NULL; in p7_domaindef_Create()
86 ESL_ALLOC(ddef->mocc, sizeof(float) * (Lalloc+1)); in p7_domaindef_Create()
90 ddef->mocc[0] = ddef->etot[0] = ddef->btot[0] = 0.; in p7_domaindef_Create()
156 ESL_RALLOC(ddef->mocc, p, sizeof(float) * (L+1)); in p7_domaindef_GrowTo()
256 fprintf(ofp, "%d %f\n", i, ddef->mocc[i]); in p7_domaindef_DumpPosteriors()
288 if (ddef->mocc != NULL) free(ddef->mocc); in p7_domaindef_Destroy()
414 if (ddef->mocc[j] - (ddef->btot[j] - ddef->btot[j-1]) < ddef->rt2) i = j; in p7_domaindef_ByPosteriorHeuristics()
416 if (ddef->mocc[j] >= ddef->rt1) triggered = TRUE; in p7_domaindef_ByPosteriorHeuristics()
418 else if (ddef->mocc[j] - (ddef->etot[j] - ddef->etot[j-1]) < ddef->rt2) in p7_domaindef_ByPosteriorHeuristics()
/dports/science/nwchem/nwchem-7b21660b82ebd85ef659f6fba7e1e73433b0bd0a/src/mrpt/fci/
H A Dfci_spnad.F31 integer mocc(nsmax) ! determinant walk
63 call fci_mfind_occ(mwalk,mocc,ns)
68 dsum = dsum + 1.5d0 - dble(mocc(is))
73 if (mocc(is).eq.1) then
81 if (mocc(is).eq.1) then
137 integer mocc(nsmax) ! determinant walk
169 call fci_mfind_occ(mwalk,mocc,ns)
174 dsum = dsum + 1.5d0 - dble(mocc(is))
179 if (mocc(is).eq.1) then
187 if (mocc(is).eq.1) then
H A Dfci.F151 integer iocc(nactmx), mocc(nsmax)
170 call fci_mfind_occ(mwalk, mocc, ns)
174 $ (spin(mocc(i)),i=1,ns)
/dports/science/nwchem-data/nwchem-7.0.2-release/src/mrpt/fci/
H A Dfci_spnad.F31 integer mocc(nsmax) ! determinant walk
63 call fci_mfind_occ(mwalk,mocc,ns)
68 dsum = dsum + 1.5d0 - dfloat(mocc(is))
73 if (mocc(is).eq.1) then
81 if (mocc(is).eq.1) then
137 integer mocc(nsmax) ! determinant walk
169 call fci_mfind_occ(mwalk,mocc,ns)
174 dsum = dsum + 1.5d0 - dfloat(mocc(is))
179 if (mocc(is).eq.1) then
187 if (mocc(is).eq.1) then
H A Dfci.F151 integer iocc(nactmx), mocc(nsmax)
170 call fci_mfind_occ(mwalk, mocc, ns)
174 $ (spin(mocc(i)),i=1,ns)
/dports/science/madness/madness-ebb3fd7/src/apps/moldft/fci/
H A Dfci_spnad.F31 integer mocc(nsmax) ! determinant walk
63 call fci_mfind_occ(mwalk,mocc,ns)
68 dsum = dsum + 1.5d0 - dfloat(mocc(is))
73 if (mocc(is).eq.1) then
81 if (mocc(is).eq.1) then
137 integer mocc(nsmax) ! determinant walk
169 call fci_mfind_occ(mwalk,mocc,ns)
174 dsum = dsum + 1.5d0 - dfloat(mocc(is))
179 if (mocc(is).eq.1) then
187 if (mocc(is).eq.1) then
H A Dfci_prvec.F14 integer iocc(nactmx), mocc(nsmax)
33 call fci_mfind_occ(mwalk, mocc, ns)
37 $ (spin(mocc(i)),i=1,ns)
/dports/science/py-pyscf/pyscf-2.0.1/pyscf/hessian/
H A Drhf.py71 mocc = mo_coeff[:,mo_occ>0]
80 s1oo = numpy.einsum('xpq,pi,qj->xij', s1ao, mocc, mocc)
119 mocc = mo_coeff[:,mo_occ>0]
120 dm0 = numpy.dot(mocc, mocc.T) * 2
122 dme0 = numpy.einsum('pi,qi,i->pq', mocc, mocc, mo_energy[mo_occ>0]) * 2
218 mocc = mo_coeff[:,mo_occ>0]
219 dm0 = numpy.dot(mocc, mocc.T) * 2
309 nocc = mocc.shape[1]
365 nocc = mocc.shape[1]
417 nocc = mocc.shape[1]
[all …]
/dports/science/nwchem/nwchem-7b21660b82ebd85ef659f6fba7e1e73433b0bd0a/src/selci/
H A Dupkcon.F12 subroutine selci_upkcon(norbs, iocc, mocc, nintpo, nbitpi) argument
17 dimension iocc(norbs), mocc(nintpo)
37 itemp = mocc(iword)
H A Dpkcon.F16 subroutine selci_pkcon(norbs, iocc, mocc, nintpo, nbitpi) argument
28 integer mocc(nintpo) !< [Output] The compressed electron
59 mocc(iword) = itemp
/dports/science/nwchem-data/nwchem-7.0.2-release/src/selci/
H A Dupkcon.F12 subroutine selci_upkcon(norbs, iocc, mocc, nintpo, nbitpi) argument
17 dimension iocc(norbs), mocc(nintpo)
37 itemp = mocc(iword)
H A Dpkcon.F16 subroutine selci_pkcon(norbs, iocc, mocc, nintpo, nbitpi) argument
28 integer mocc(nintpo) !< [Output] The compressed electron
59 mocc(iword) = itemp
/dports/x11-drivers/xf86-video-nv/xf86-video-nv-2.1.21/src/
H A Driva_hw.c122 int mocc; member
187 if (ainfo->wcmocc > ainfo->mocc) ainfo->wcmocc = ainfo->mocc; in nv3_iterate()
201 else if (ainfo->mocc < 0) in nv3_iterate()
213 else if (ainfo->mocc<0) in nv3_iterate()
222 else if (ainfo->mocc<0) in nv3_iterate()
227 if (ainfo->mocc<0) in nv3_iterate()
255 ainfo->mocc = ainfo->mocc - ns*ainfo->mdrain_rate/1000000; in nv3_iterate()
271 ainfo->mocc = ainfo->mocc + 0 - ns*ainfo->mdrain_rate/1000000; in nv3_iterate()
281 ainfo->mocc = ainfo->mocc + mburst_size - ns*ainfo->mdrain_rate/1000000; in nv3_iterate()
313 if (ABS(ainfo->mocc) > MFIFO_SIZE) in nv3_iterate()
[all …]
/dports/science/py-pyscf/pyscf-2.0.1/pyscf/eph/
H A Drhf.py105 mocc = mo_coeff[:,mo_occ>0]
106 nocc = mocc.shape[1]
113 dm = np.dot(x*2, mocc.T) # *2 for double occupancy
150 mocc = mf.mo_coeff[:,mf.mo_occ>0]
151 dm0 = np.dot(mocc, mocc.T) * 2
H A Drks.py116 mocc = mf.mo_coeff[:,mf.mo_occ>0]
117 dm0 = np.dot(mocc, mocc.T) * 2
/dports/science/py-pyscf/pyscf-2.0.1/pyscf/df/hessian/
H A Drhf.py67 mocc = mo_coeff[:,mo_occ>0]
68 mocc_2 = np.einsum('pi,i->pi', mocc, mo_occ[mo_occ>0]**.5)
69 nocc = mocc.shape[1]
70 dm0 = numpy.dot(mocc, mocc.T) * 2
72 dme0 = numpy.einsum('pi,qi,i->pq', mocc, mocc, mo_energy[mo_occ>0]) * 2
391 mocc = mo_coeff[:,mo_occ>0]
392 nocc = mocc.shape[1]
393 mocc_2 = np.einsum('pi,i->pi', mocc, mo_occ[mo_occ>0]**.5)
394 dm0 = numpy.dot(mocc, mocc.T) * 2
H A Drks.py50 mocc = mo_coeff[:,mo_occ>0]
51 dm0 = numpy.dot(mocc, mocc.T) * 2
/dports/multimedia/libv4l/linux-5.13-rc2/drivers/video/fbdev/riva/
H A Driva_hw.c172 int mocc; member
278 if (ainfo->wcmocc > ainfo->mocc) ainfo->wcmocc = ainfo->mocc; in nv3_iterate()
292 else if (ainfo->mocc < 0) in nv3_iterate()
304 else if (ainfo->mocc<0) in nv3_iterate()
313 else if (ainfo->mocc<0) in nv3_iterate()
318 if (ainfo->mocc<0) in nv3_iterate()
346 ainfo->mocc = ainfo->mocc - ns*ainfo->mdrain_rate/1000000; in nv3_iterate()
362 ainfo->mocc = ainfo->mocc + 0 - ns*ainfo->mdrain_rate/1000000; in nv3_iterate()
372 ainfo->mocc = ainfo->mocc + mburst_size - ns*ainfo->mdrain_rate/1000000; in nv3_iterate()
404 if (abs(ainfo->mocc) > MFIFO_SIZE) in nv3_iterate()
[all …]
/dports/multimedia/v4l_compat/linux-5.13-rc2/drivers/video/fbdev/riva/
H A Driva_hw.c172 int mocc; member
278 if (ainfo->wcmocc > ainfo->mocc) ainfo->wcmocc = ainfo->mocc; in nv3_iterate()
292 else if (ainfo->mocc < 0) in nv3_iterate()
304 else if (ainfo->mocc<0) in nv3_iterate()
313 else if (ainfo->mocc<0) in nv3_iterate()
318 if (ainfo->mocc<0) in nv3_iterate()
346 ainfo->mocc = ainfo->mocc - ns*ainfo->mdrain_rate/1000000; in nv3_iterate()
362 ainfo->mocc = ainfo->mocc + 0 - ns*ainfo->mdrain_rate/1000000; in nv3_iterate()
372 ainfo->mocc = ainfo->mocc + mburst_size - ns*ainfo->mdrain_rate/1000000; in nv3_iterate()
404 if (abs(ainfo->mocc) > MFIFO_SIZE) in nv3_iterate()
[all …]
/dports/multimedia/v4l-utils/linux-5.13-rc2/drivers/video/fbdev/riva/
H A Driva_hw.c172 int mocc; member
278 if (ainfo->wcmocc > ainfo->mocc) ainfo->wcmocc = ainfo->mocc; in nv3_iterate()
292 else if (ainfo->mocc < 0) in nv3_iterate()
304 else if (ainfo->mocc<0) in nv3_iterate()
313 else if (ainfo->mocc<0) in nv3_iterate()
318 if (ainfo->mocc<0) in nv3_iterate()
346 ainfo->mocc = ainfo->mocc - ns*ainfo->mdrain_rate/1000000; in nv3_iterate()
362 ainfo->mocc = ainfo->mocc + 0 - ns*ainfo->mdrain_rate/1000000; in nv3_iterate()
372 ainfo->mocc = ainfo->mocc + mburst_size - ns*ainfo->mdrain_rate/1000000; in nv3_iterate()
404 if (abs(ainfo->mocc) > MFIFO_SIZE) in nv3_iterate()
[all …]

12