/dports/biology/infernal/infernal-1.1.3/hmmer/src/ |
H A D | modelstats.c | 166 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 …]
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H A D | p7_hmm.c | 627 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 …]
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H A D | p7_domaindef.c | 79 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()
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/dports/biology/hmmer/hmmer-3.3/src/ |
H A D | modelstats.c | 166 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 …]
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H A D | p7_hmm.c | 627 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 …]
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H A D | p7_domaindef.c | 79 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()
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/dports/science/nwchem/nwchem-7b21660b82ebd85ef659f6fba7e1e73433b0bd0a/src/mrpt/fci/ |
H A D | fci_spnad.F | 31 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
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H A D | fci.F | 151 integer iocc(nactmx), mocc(nsmax) 170 call fci_mfind_occ(mwalk, mocc, ns) 174 $ (spin(mocc(i)),i=1,ns)
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/dports/science/nwchem-data/nwchem-7.0.2-release/src/mrpt/fci/ |
H A D | fci_spnad.F | 31 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
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H A D | fci.F | 151 integer iocc(nactmx), mocc(nsmax) 170 call fci_mfind_occ(mwalk, mocc, ns) 174 $ (spin(mocc(i)),i=1,ns)
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/dports/science/madness/madness-ebb3fd7/src/apps/moldft/fci/ |
H A D | fci_spnad.F | 31 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
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H A D | fci_prvec.F | 14 integer iocc(nactmx), mocc(nsmax) 33 call fci_mfind_occ(mwalk, mocc, ns) 37 $ (spin(mocc(i)),i=1,ns)
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/dports/science/py-pyscf/pyscf-2.0.1/pyscf/hessian/ |
H A D | rhf.py | 71 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 …]
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/dports/science/nwchem/nwchem-7b21660b82ebd85ef659f6fba7e1e73433b0bd0a/src/selci/ |
H A D | upkcon.F | 12 subroutine selci_upkcon(norbs, iocc, mocc, nintpo, nbitpi) argument 17 dimension iocc(norbs), mocc(nintpo) 37 itemp = mocc(iword)
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H A D | pkcon.F | 16 subroutine selci_pkcon(norbs, iocc, mocc, nintpo, nbitpi) argument 28 integer mocc(nintpo) !< [Output] The compressed electron 59 mocc(iword) = itemp
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/dports/science/nwchem-data/nwchem-7.0.2-release/src/selci/ |
H A D | upkcon.F | 12 subroutine selci_upkcon(norbs, iocc, mocc, nintpo, nbitpi) argument 17 dimension iocc(norbs), mocc(nintpo) 37 itemp = mocc(iword)
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H A D | pkcon.F | 16 subroutine selci_pkcon(norbs, iocc, mocc, nintpo, nbitpi) argument 28 integer mocc(nintpo) !< [Output] The compressed electron 59 mocc(iword) = itemp
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/dports/x11-drivers/xf86-video-nv/xf86-video-nv-2.1.21/src/ |
H A D | riva_hw.c | 122 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 …]
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/dports/science/py-pyscf/pyscf-2.0.1/pyscf/eph/ |
H A D | rhf.py | 105 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
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H A D | rks.py | 116 mocc = mf.mo_coeff[:,mf.mo_occ>0] 117 dm0 = np.dot(mocc, mocc.T) * 2
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/dports/science/py-pyscf/pyscf-2.0.1/pyscf/df/hessian/ |
H A D | rhf.py | 67 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
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H A D | rks.py | 50 mocc = mo_coeff[:,mo_occ>0] 51 dm0 = numpy.dot(mocc, mocc.T) * 2
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/dports/multimedia/libv4l/linux-5.13-rc2/drivers/video/fbdev/riva/ |
H A D | riva_hw.c | 172 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 …]
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/dports/multimedia/v4l_compat/linux-5.13-rc2/drivers/video/fbdev/riva/ |
H A D | riva_hw.c | 172 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 …]
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/dports/multimedia/v4l-utils/linux-5.13-rc2/drivers/video/fbdev/riva/ |
H A D | riva_hw.c | 172 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 …]
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