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NWChem: Open Source High-Performance Computational Chemistry
GitHub
commit
2f7ab4a93a
22 changed files with 22715 additions and 313 deletions
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@ -736,6 +736,8 @@ let "myexit+=$?"
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let "myexit+=$?"
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./runtests.mpi.unix procs $np dft_nio_r2scan
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let "myexit+=$?"
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./runtests.mpi.unix procs $np cosmo_h2cco2_opt
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let "myexit+=$?"
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if [[ "$what" != "flaky" ]]; then
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echo
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echo "the number of failed tests is" $myexit
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81
QA/tests/cosmo_h2cco2_opt/cosmo_h2cco2_opt.nw
Normal file
81
QA/tests/cosmo_h2cco2_opt/cosmo_h2cco2_opt.nw
Normal file
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@ -0,0 +1,81 @@
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echo
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start
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geometry
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o 0.00000000 -1.11909860 -0.09529177
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o 0.00000000 1.11909860 -0.09529177
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c 0.00000000 0.00000000 0.66838924
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c 0.00000000 0.00000000 1.99717688
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h 0.00000000 -0.92756722 2.53578926
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h 0.00000000 0.92756722 2.53578926
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end
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charge -2
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basis spherical
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* library 6-31g*
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end
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title "new potential"
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cosmo
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potcorr true
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ificos 1 ; minbem 3
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do_gasphase f
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end
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driver
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maxiter 99
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clear
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end
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dft
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xc hfexch
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end
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task dft optimize
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title "old potential"
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geometry
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o 0.00000000 -1.11909860 -0.09529177
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o 0.00000000 1.11909860 -0.09529177
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c 0.00000000 0.00000000 0.66838924
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c 0.00000000 0.00000000 1.99717688
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h 0.00000000 -0.92756722 2.53578926
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h 0.00000000 0.92756722 2.53578926
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end
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cosmo
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potcorr false
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do_gasphase f
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ificos 1 ; minbem 3
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print cosmo_energies
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end
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driver
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clear
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end
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task scf optimize ignore
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title "GEPOL cavity"
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geometry
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o 0.00000000 -1.11909860 -0.09529177
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o 0.00000000 1.11909860 -0.09529177
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c 0.00000000 0.00000000 0.66838924
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c 0.00000000 0.00000000 1.99717688
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h 0.00000000 -0.92756722 2.53578926
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h 0.00000000 0.92756722 2.53578926
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end
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cosmo
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do_gasphase f
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cavity ses
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ndiv xfine
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end
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unset cosmo:ptcor
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driver
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clear
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end
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task scf optimize ignore
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19581
QA/tests/cosmo_h2cco2_opt/cosmo_h2cco2_opt.out
Normal file
19581
QA/tests/cosmo_h2cco2_opt/cosmo_h2cco2_opt.out
Normal file
File diff suppressed because it is too large
Load diff
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@ -173,7 +173,8 @@ c
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call ga_zero(g_dens)
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call ga_copy(g_cdens,g_dens)
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if (nopen.gt.0) call ga_add(1.d0,g_cdens,one,g_odens,g_dens)
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call cosmo_charges_from_dmat(rtdb, basis, geom, ecosmo, odebug,
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call cosmo_charges_from_dmat(rtdb, basis, geom,
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& ecosmo, 0d0, 0d0, odebug,
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& 1, ! 1 = closed shell
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& g_dens, ! input density
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& cosmo_file) ! cosmo charges file name
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@ -1152,7 +1152,8 @@ c check if we are doing dft (e.g. cphf case)
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end do
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call ga_copy(g_a_dens,g_dens(1)) ! alpha = 1
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call ga_copy(g_b_dens,g_dens(2)) ! beta = 2
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call cosmo_charges_from_dmat(rtdb, basis, geom, ecosmo, odebug,
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call cosmo_charges_from_dmat(rtdb, basis, geom,
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& ecosmo, 0d0, energy, odebug,
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& 2, ! 2 = open shell
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& g_dens, ! input density
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& cosmo_file) ! cosmo charges file name
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@ -23,14 +23,11 @@ include ../config/makelib.h
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ifeq ($(_FC),pgf90)
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FOPTIONS += -Mnorecursive
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endif
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ifeq ($(FC),gfortran)
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ifdef USE_OPENMP
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FOPTIONS += -fno-recursive -fno-openmp
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endif
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endif
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ifeq ($(_FC),gfortran)
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ifdef USE_OPENMP
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FOPTIONS += -fno-recursive -fno-openmp
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ifneq ($(FLANG_NEW),true)
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FOPTIONS += -fno-recursive -fno-openmp
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endif
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endif
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endif
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ifeq ($(FC),pathf90)
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@ -754,7 +754,7 @@ c if (oroot) write(luout,*) "calling cosmo_charges_from_dmat"
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call cosmo_charges_from_dmat(rtdb,
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& ihdl_bfao,
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& ihdl_geom,
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& ecosmo,
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& ecosmo, 0d0, 0d0,
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& odbug, ! debug
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& 1, ! up and down are combined
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& g_p_ao, ! input density
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@ -259,6 +259,7 @@ c == initialize DIIS call counter ==
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c
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gcds = 0.d0
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egas = 0d0
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esol = 0d0
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do_cosmo_vem = 0
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istep_cosmo_vem = 0
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do_cosmo_smd = .false.
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@ -1198,8 +1199,8 @@ c
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cosmo_file = 'cosmo.xyz'
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if (ipol.eq.2) ! separate components
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& call ga_dadd(1.d0,g_dens(1),-1.d0,g_dens(2),g_dens(1))
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call cosmo_charges_from_dmat(rtdb, ao_bas_han, geom,
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& ecosmo, odbug, ipol, g_dens, cosmo_file)
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call cosmo_charges_from_dmat(rtdb, ao_bas_han, geom, ecosmo,
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& egas, etnew+enuc, odbug, ipol, g_dens, cosmo_file)
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if (ipol.eq.2) ! reinstate total
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& call ga_dadd(one, g_dens(1), one, g_dens(2), g_dens(1))
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end if ! cosmo check
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@ -2192,8 +2193,8 @@ c
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cosmo_file = 'cosmo.xyz'
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if(ipol.eq.2) ! separate components
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& call ga_dadd(1.d0,g_dens(1),-1.d0,g_dens(2),g_dens(1))
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call cosmo_charges_from_dmat(rtdb, ao_bas_han, geom,
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& ecosmo, odbug, ipol, g_dens, cosmo_file)
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call cosmo_charges_from_dmat(rtdb, ao_bas_han, geom, ecosmo,
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& egas, esol, odbug, ipol, g_dens, cosmo_file)
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if (ipol.eq.2) ! reinstate total in g_dens(1)
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& call ga_dadd(one, g_dens(1), one, g_dens(2), g_dens(1))
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end if ! cosmo_esp
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@ -274,7 +274,8 @@ c
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call ga_zero(g_dens)
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call ga_copy(g_cdens,g_dens)
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if (nopen.gt.0) call ga_add(1.d0,g_cdens,one,g_odens,g_dens)
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call cosmo_charges_from_dmat(rtdb, basis, geom, ecosmo, odebug,
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call cosmo_charges_from_dmat(rtdb, basis, geom,
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& ecosmo, 0d0, 0d0, odebug,
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& 1, ! 1 = closed shell
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& g_dens, ! input density
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& cosmo_file) ! cosmo charges file name
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@ -348,7 +348,8 @@ c
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end do
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call ga_copy(g_a_dens,g_dens(1)) ! alpha = 1
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call ga_copy(g_b_dens,g_dens(2)) ! beta = 2
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call cosmo_charges_from_dmat(rtdb, basis, geom, ecosmo, odebug,
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call cosmo_charges_from_dmat(rtdb, basis, geom,
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& ecosmo, 0d0, energy, odebug,
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& 2, ! 2 = open shell
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& g_dens, ! input density
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& cosmo_file) ! cosmo charges file name
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@ -1268,7 +1268,7 @@ c Calculate cosmo charges
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if (cosmo_on.and.cosmo_phase.eq.2) then
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cosmo_file = "cosmo.xyz"
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call cosmo_charges_from_dmat(rtdb, ao_bas_han, geom,
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& ecosmo, odbug, ipol, g_dens, cosmo_file)
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& ecosmo, egas, etnew+enuc, odbug, ipol, g_dens, cosmo_file)
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call cosmo_fock(ao_bas_han, g_fock)
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call ga_dadd(one, g_dens(1), one, g_dens(2), g_dens(1))
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Ecore = ga_ddot(g_dens(1), g_fock)
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@ -8,15 +8,18 @@
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cosmo_smd_output.o\
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cosmo_vem_output.o\
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cosmo_lebedev.o\
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cosmo_fibonacci.o
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OBJ_OPTIMIZE = cosmo_input.o \
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cosmo_fibonacci.o\
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hnd_cosmo_lib.o hnd_coschg.o\
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cosmo_input.o \
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cosmo_initialize.o\
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cosmo_tidy.o\
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cosmo_def_radii.o\
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cosmo_charges.o\
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grad_hnd_cos.o hnd_cosmo_lib.o hnd_coschg.o\
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gepol_lib.o\
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grad_hnd_cos.o\
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cosmo_thomson.o
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OBJ_OPTIMIZE =
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LIBRARY = libsolvation.a
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@ -34,4 +37,7 @@ HEADERS = ../property/prop.fh ../property/atomdata.fh cosmoP.fh cosmo_params.fh
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include ../config/makefile.h
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include ../config/makelib.h
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ifeq ($(FLANG_NEW),true)
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FOPTIONS += -fno-automatic
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endif
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#FDEBUG += -O0
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@ -44,3 +44,12 @@ c
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integer COSMO_LINEQ_ITERATIVE
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parameter (COSMO_LINEQ_DIRECT = 0)
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parameter (COSMO_LINEQ_ITERATIVE = 1)
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c
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c COSMO cavity type
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c - COSMO_CAVITY_VDW : Use a van der Waals cavity
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c - COSMO_CAVITY_SES : Use a solvent-excluded cavity
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c
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integer COSMO_CAVITY_VDW
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integer COSMO_CAVITY_SES
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parameter (COSMO_CAVITY_VDW = 0)
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parameter (COSMO_CAVITY_SES = 1)
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@ -5,225 +5,11 @@ C>
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C> \file cosmo_charges.F
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C> The COSMO surface generator
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C>
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C> \brief Compute the COSMO charges
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C>
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subroutine cosmo_charges(rtdb,basis,geom,ecos,some,
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& itype_wfn,vectors,nclosed,nopen,nbf,nmo)
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c
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implicit none
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c
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#include "errquit.fh"
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#include "global.fh"
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#include "geom.fh"
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#include "rtdb.fh"
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#include "util.fh"
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#include "mafdecls.fh"
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#include "nwc_const.fh"
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#include "stdio.fh"
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#include "prop.fh"
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#include "cosmoP.fh"
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#include "cosmo_params.fh"
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#include "util_params.fh"
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c
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integer rtdb !< [Input] The RTDB handle
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integer basis !< [Input] The basis set handle
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integer geom !< [Input] The geometry handle
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integer nbf !< [Input] The number of basis functions
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integer nmo !< [Input] The number of molecular orbitals
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integer itype_wfn !< [Input] The wavefunction type
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!< - 1: RHF type wavefunction
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!< - 2: UHF type wavefunction
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integer vectors(2) !< [Input] The GA handles for the SCF vectors
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integer nclosed(2) !< [Input] The number of closed shell orbitals
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!< (only used with RHF)
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integer nopen(2) !< [Input] The number of open shell orbitals
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c
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double precision ecos !< [Output] The intra COSMO charges
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!< interaction energy
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logical some !< [Input] Do you want "some" additional output?
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logical dbug, out, status
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character*8 scfruntyp
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c
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character*255 cosmo_file
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c
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c
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integer l_efcc, k_efcc, l_efcs, k_efcs, l_efcz, k_efcz
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integer l_msrf, k_msrf
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integer l_efciat, k_efciat
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integer l_rad, k_rad, nrad
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integer l_occ, k_occ
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integer l_efczz, k_efczz
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integer nefc, ief, i, nat
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integer g_dens(3) ! 1: up, 2: down, 3: total
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integer ndens,nvirt(2)
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logical stat
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c
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c
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integer ga_create_atom_blocked
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external ga_create_atom_blocked
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c
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dbug=.false..and.ga_nodeid().eq.0
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out =.false..and.ga_nodeid().eq.0
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out =out.or.dbug
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some=some.or.out.and.ga_nodeid().eq.0
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c
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if(some) then
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write(luout,9999)
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endif
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c
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if(out) then
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write(luout,*) 'in cosmo_charges ... geom = ',geom
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endif
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c
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c ----- retrieve the number of atoms from -geom- -----
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c
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if (.not.geom_ncent(geom,nat))
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& call errquit("cosmo_charges: geom_ncent failed",0,UERR)
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c
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c ----- read -efc- coordinates from -rtdb- -----
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c
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if(.not.rtdb_get(rtdb,'cosmo:nefc',mt_int,1 ,nefc))
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& call errquit('cosmo_charges: rtdb get failed for nefc ',911,
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& RTDB_ERR)
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c
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c ----- allocate memory for efc's -----
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c
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if(.not.ma_push_get(mt_dbl,nefc*3,'cosmo efcc',l_efcc,k_efcc))
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& call errquit('cosmo_charges malloc k_efcc failed',911,MA_ERR)
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if(.not.ma_push_get(mt_dbl,nefc,'cosmo efcs',l_efcs,k_efcs))
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& call errquit('cosmo_charges malloc k_efcs failed',911,MA_ERR)
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if(.not.ma_push_get(mt_dbl,nefc,'molsurf',l_msrf,k_msrf))
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& call errquit('cosmo_charges malloc k_msrf failed',911,MA_ERR)
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if(.not.ma_push_get(mt_dbl,nefc,'cosmo efcz',l_efcz,k_efcz))
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& call errquit('cosmo_charges malloc k_efcz failed',911,MA_ERR)
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if(.not.ma_push_get(mt_dbl,nefc,'cosmo efczz',l_efczz,k_efczz))
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& call errquit('cosmo_charges malloc k_efczz failed',911,MA_ERR)
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if(.not.ma_push_get(mt_int,nefc,'cosmo efciat',l_efciat,k_efciat))
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& call errquit('cosmo_charges malloc k_efciat failed',911,MA_ERR)
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if(.not.ma_push_get(mt_dbl,nat,'cosmo rad',l_rad,k_rad))
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& call errquit('cosmo_charges malloc k_rad failed',nat,MA_ERR)
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c
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if(.not.rtdb_get(rtdb,'cosmo:efcc',mt_dbl,3*nefc,dbl_mb(k_efcc)))
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& call errquit('cosmo_charges: rtdb get failed for efcc ',912,
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& RTDB_ERR)
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if(.not.rtdb_get(rtdb,'cosmo:efcz',mt_dbl, nefc,dbl_mb(k_efcz)))
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& call errquit('cosmo_charges: rtdb get failed for efcz ',913,
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& RTDB_ERR)
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if(.not.rtdb_get(rtdb,'cosmo:efcs',mt_dbl, nefc,dbl_mb(k_efcs)))
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& call errquit('cosmo_charges: rtdb get failed for efcs ',914,
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& RTDB_ERR)
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if(.not.rtdb_get(rtdb,'cosmo:efczz',mt_dbl,nefc,dbl_mb(k_efczz)))
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& call errquit('cosmo_charges: rtdb get failed for efczz',914,
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& RTDB_ERR)
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if(.not.rtdb_get(rtdb,'cosmo:efciat',
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& mt_int,nefc,int_mb(k_efciat)))
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& call errquit('cosmo_charges: rtdb get failed for efciat',914,
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& RTDB_ERR)
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call cosmo_def_radii(rtdb,geom,nat,dbl_mb(k_rad),.false.)
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status = rtdb_get(rtdb,'cosmo:radius',mt_dbl, nat,dbl_mb(k_rad))
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do i = 0, nat-1
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dbl_mb(k_rad+i) = dbl_mb(k_rad+i)/cau2ang
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enddo
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c
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if(out) then
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write(luout,*) 'in cosmo_charges, nefc = ',nefc
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do ief=1,nefc
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write(luout,*) dbl_mb(k_efcc+(ief-1)*3),
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& dbl_mb(k_efcc+(ief-1)*3+1),dbl_mb(k_efcc+(ief-1)*3+2)
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enddo
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endif
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c
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c ----- calculate the density matrices from molecular orbitals -----
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cc
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cc ----- get density matrix -----
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cc
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c scfruntyp='RHF'
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c nocc=nclosed(1)+nopen(1)
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c if (itype_wfn.eq.2) then
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c scfruntyp='UHF'
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c nocc=max(nocc,nclosed(2)+nopen(2))
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c endif
|
||||
c if(.not.ma_push_get(mt_dbl,nocc*2,'cosmo occ',l_occ,k_occ))
|
||||
c & call errquit('cosmo_charges malloc k_occ failed',911,MA_ERR)
|
||||
c do i=1,nocc*2
|
||||
c dbl_mb(k_occ+i-1)=1.0d0
|
||||
c enddo
|
||||
c
|
||||
c changes to make cosmo work for open shell DFT (MV)
|
||||
c
|
||||
if(.not.ma_push_get(mt_dbl,nbf*2,'cosmo occ',l_occ,k_occ))
|
||||
& call errquit('cosmo_charges malloc k_occ failed',911,MA_ERR)
|
||||
call dfill(2*nbf, 0.0d0, dbl_mb(k_occ), 1)
|
||||
c
|
||||
c Only need to set occupation numbers for UHF
|
||||
c occupation numbers for RHF are done inside hnd_prop_dens_make
|
||||
c
|
||||
if (itype_wfn.eq.2) then
|
||||
scfruntyp='UHF'
|
||||
do i = 1, nopen(1)
|
||||
dbl_mb(i-1+k_occ) = 1.0d0
|
||||
enddo
|
||||
do i = nbf+1, nbf+nopen(2)
|
||||
dbl_mb(i-1+k_occ) = 1.0d0
|
||||
enddo
|
||||
else if (itype_wfn.eq.1) then
|
||||
scfruntyp='RHF'
|
||||
do i = 1, nclosed(1)
|
||||
dbl_mb(i-1+k_occ) = 2.0d0
|
||||
enddo
|
||||
do i = nclosed(1)+1, nclosed(1)+nopen(1)
|
||||
dbl_mb(i-1+k_occ) = 1.0d0
|
||||
enddo
|
||||
else
|
||||
call errquit("unknown function type",0,0)
|
||||
endif
|
||||
c
|
||||
c end of changes (MV)
|
||||
c
|
||||
call hnd_prop_dens_make(rtdb,geom,basis,nbf,nmo,nclosed,nopen,
|
||||
& nvirt,scfruntyp,vectors,dbl_mb(k_occ),
|
||||
& g_dens,ndens)
|
||||
c
|
||||
if(out) then
|
||||
write(luout,*) 'in -cosmo_charges, wfntyp = ',itype_wfn
|
||||
write(luout,*) 'in -cosmo_charges, scftyp = ',scfruntyp
|
||||
if(dbug) then
|
||||
write(luout,*) 'in -cosmo_charges, -da- ...'
|
||||
call ga_print(g_dens(1))
|
||||
if(scfruntyp.eq.'UHF ') then
|
||||
write(luout,*) 'in -cosmo_charges, -db- ...'
|
||||
call ga_print(g_dens(2))
|
||||
endif
|
||||
endif ! dbug
|
||||
endif !out
|
||||
c
|
||||
c ----- get -cosmo- charges -----
|
||||
c
|
||||
call hnd_coschg(g_dens,ndens,rtdb,geom,basis,nat,nefc,
|
||||
& dbl_mb(k_efcc),dbl_mb(k_efcs),dbl_mb(k_msrf),
|
||||
& dbl_mb(k_efcz),dbl_mb(k_efczz),
|
||||
& int_mb(k_efciat),dbl_mb(k_rad),ecos,cosmo_file)
|
||||
c
|
||||
c ----- release memory block -----
|
||||
c
|
||||
do i = 1, ndens
|
||||
if (.not.ga_destroy(g_dens(i))) call
|
||||
& errquit('cosmo_charges: ga_destroy failed g_dens',0,GA_ERR)
|
||||
enddo
|
||||
if(.not.ma_chop_stack(l_efcc))
|
||||
& call errquit('cosmo_charges, ma_chop_stack of l_efcc failed',911,
|
||||
& ma_err)
|
||||
c
|
||||
return
|
||||
9999 format(/,10X,15(1H-),
|
||||
1 /,10X,'-cosmo- charges',
|
||||
2 /,10X,15(1H-))
|
||||
end
|
||||
c
|
||||
C> \brief Compute the COSMO charges from an input density matrix
|
||||
c
|
||||
subroutine cosmo_charges_from_dmat(rtdb,basis,geom,ecos,some,
|
||||
& ipol,g_dens_in,cosmo_file)
|
||||
subroutine cosmo_charges_from_dmat(rtdb,basis,geom,
|
||||
& ecos,egas,esol,
|
||||
& some,ipol,g_dens_in,cosmo_file)
|
||||
c
|
||||
implicit none
|
||||
c
|
||||
|
|
@ -241,6 +27,8 @@ c
|
|||
integer basis !< [Input] The basis set handle
|
||||
integer geom !< [Input] The geometry handle
|
||||
double precision ecos !< [Output] The intra COSMO charges, interaction energy
|
||||
double precision egas !< [Input] The total gas energy
|
||||
double precision esol !< [Input] The total solvated energy
|
||||
logical some !< [Input] Do you want "some" additional output?
|
||||
integer ipol !< [Input] 1: RHF type wavefunction, 2: UHF type wavefunction
|
||||
integer g_dens_in(ipol) !< [Input] 1: up, 2: down (input density matrix to get the charges)
|
||||
|
|
@ -374,7 +162,8 @@ c
|
|||
call hnd_coschg(g_dens,ndens,rtdb,geom,basis,nat,nefc,
|
||||
& dbl_mb(k_efcc),dbl_mb(k_efcs),dbl_mb(k_msrf),
|
||||
& dbl_mb(k_efcz),dbl_mb(k_efczz),
|
||||
& int_mb(k_efciat),dbl_mb(k_rad),ecos,cosmo_file)
|
||||
& int_mb(k_efciat),dbl_mb(k_rad),
|
||||
& ecos,egas,esol,cosmo_file)
|
||||
c
|
||||
c ----- release memory block -----
|
||||
c
|
||||
|
|
|
|||
|
|
@ -36,7 +36,7 @@ c
|
|||
logical status
|
||||
logical cosmo
|
||||
c
|
||||
integer iat, nrad, cosmo_screen
|
||||
integer iat, nrad, cosmo_screen, cosmo_cavity
|
||||
integer l_rad, k_rad, l_costag, k_costag, l_coszan, k_coszan
|
||||
integer l_coscoor, k_coscoor
|
||||
integer invnuc, nat, nefc, nmap
|
||||
|
|
@ -251,9 +251,11 @@ c
|
|||
if(.not.ma_pop_stack(l_costag)) call
|
||||
& errquit('cosmo_init,ma_pop_stack of l_tag failed',911, MA_ERR)
|
||||
c
|
||||
do_cosmo_model = DO_COSMO_YK
|
||||
if(.not.rtdb_get(rtdb,'cosmo:dielec',mt_dbl,1,dielec))
|
||||
D dielec =78.4d0 ! default water dielectric
|
||||
cosmo_cavity = COSMO_CAVITY_VDW
|
||||
if(.not.rtdb_get(rtdb,'cosmo:cavity',mt_int,1,cosmo_cavity))
|
||||
D cosmo_cavity = COSMO_CAVITY_VDW
|
||||
cosmo_screen = COSMO_SCREEN_ST
|
||||
cosmo_sccor = COSMO_SCCOR_LAGRA ! surface charge correction adapted for geometry optimzations
|
||||
minbem =2
|
||||
|
|
@ -285,8 +287,9 @@ c
|
|||
c
|
||||
status = rtdb_get(rtdb,'slv:cosmo',mt_log,1,cosmo)
|
||||
status = rtdb_get(rtdb,'cosmo:rsolv',mt_dbl,1,rsolv)
|
||||
status = rtdb_get(rtdb,'cosmo:do_cosmo_model',mt_int,1,
|
||||
+ do_cosmo_model)
|
||||
if(.not.rtdb_get(rtdb,'cosmo:do_cosmo_model',mt_int,1,
|
||||
+ do_cosmo_model))
|
||||
C do_cosmo_model=DO_COSMO_YK
|
||||
if (do_cosmo_model.eq.DO_COSMO_KS) then
|
||||
cosmo_sccor = COSMO_SCCOR_SCALE
|
||||
cosmo_screen = COSMO_SCREEN_KS
|
||||
|
|
@ -296,6 +299,8 @@ c
|
|||
endif
|
||||
status = rtdb_get(rtdb,'cosmo:screen',mt_int,1,cosmo_screen)
|
||||
status = rtdb_get(rtdb,'cosmo:sccor',mt_int,1,cosmo_sccor)
|
||||
if(.not.rtdb_get(rtdb,'cosmo:ptcor',mt_log,1,cosmo_ptcor))
|
||||
I cosmo_ptcor = .false. ! correct potentials in case of outlying charge corrections
|
||||
status = rtdb_get(rtdb,'cosmo:minbem',mt_int,1,minbem)
|
||||
status = rtdb_get(rtdb,'cosmo:maxbem',mt_int,1,maxbem)
|
||||
status = rtdb_get(rtdb,'cosmo:ificos',mt_int,1,ificos)
|
||||
|
|
@ -506,6 +511,7 @@ c
|
|||
write(Luout,9999)
|
||||
if (do_cosmo_model.eq.DO_COSMO_KS) then
|
||||
write(Luout,9970)
|
||||
if (cosmo_cavity.eq.COSMO_CAVITY_SES) write (Luout,8870)
|
||||
else if (do_cosmo_model.eq.DO_COSMO_YK) then
|
||||
write(Luout,9971)
|
||||
endif
|
||||
|
|
@ -608,15 +614,17 @@ c
|
|||
if(osome.and.me.eq.0) then
|
||||
write(luout,9993) lineq
|
||||
if ((iangleb.lt.1).and.(fibonacci.lt.1)) then
|
||||
write(luout,9991) minbem
|
||||
if (do_cosmo_model.eq.DO_COSMO_KS) then
|
||||
write(luout,9992) maxbem
|
||||
endif
|
||||
if(ificos.eq.0) then
|
||||
write(luout,9990)
|
||||
else
|
||||
write(luout,9989)
|
||||
endif
|
||||
if (cosmo_cavity.ne.COSMO_CAVITY_SES) then
|
||||
write(luout,9991) minbem
|
||||
if (do_cosmo_model.eq.DO_COSMO_KS) then
|
||||
write(luout,9992) maxbem
|
||||
endif
|
||||
if(ificos.eq.0) then
|
||||
write(luout,9990)
|
||||
else
|
||||
write(luout,9989)
|
||||
endif
|
||||
end if
|
||||
elseif (fibonacci.lt.1) then
|
||||
write(luout,9969)
|
||||
write(luout,9968) iangleb
|
||||
|
|
@ -750,6 +758,8 @@ c
|
|||
9972 format(' surface charge correction = ',a)
|
||||
9971 format(' Cosmo: York-Karplus, doi: 10.1021/jp992097l')
|
||||
9970 format(' Cosmo: Klamt-Schuurmann, doi: 10.1039/P29930000799')
|
||||
c TODO: describe the GEPOL modifications and publish a new article
|
||||
8870 format(' SES surface, doi: 10.1002/jcc.540151009, ??')
|
||||
|
||||
9969 format(' Using -Lebedev- grid')
|
||||
9968 format(' -iangleb',I4)
|
||||
|
|
|
|||
|
|
@ -72,6 +72,7 @@ c
|
|||
integer iat, nfield, nrad, irad
|
||||
integer iscren, ifscrn, minbem, maxbem, ificos, lineq
|
||||
integer cosmo_screen, cosmo_sccor
|
||||
logical cosmo_ptcor
|
||||
integer iangleb
|
||||
integer fibonacci
|
||||
integer thomson
|
||||
|
|
@ -79,6 +80,9 @@ c
|
|||
double precision dielec,dielecinf,rsolv,rad,zeta,gammas,swtol
|
||||
character*255 field
|
||||
logical do_cosmo
|
||||
integer cosmo_cavity
|
||||
integer cosmo_ndiv
|
||||
double precision mfactor
|
||||
logical do_cosmo_file
|
||||
logical do_gasphase
|
||||
logical status
|
||||
|
|
@ -136,6 +140,8 @@ c
|
|||
solvname_long = 'water'
|
||||
cosmo_screen = COSMO_SCREEN_ST
|
||||
cosmo_sccor = COSMO_SCCOR_LAGRA ! surface charge correction adapted for geometry optimzations
|
||||
cosmo_ndiv = 2 ! used with the SES cavity
|
||||
mfactor =1.00d+00 ! used with the SES cavity
|
||||
minbem =2
|
||||
maxbem =4 ! used with the Klamt-Schuurmann model
|
||||
ificos =0
|
||||
|
|
@ -311,21 +317,25 @@ c
|
|||
else if(inp_compare(.false.,'off',field)) then
|
||||
do_cosmo=.false.
|
||||
c
|
||||
c --- do_cosmo_ks: switch to Klamt-Schuurmann model
|
||||
c --- do_cosmo_ks: switch to Klamt-Schuurmann model; also makes cavity=ses
|
||||
c
|
||||
else if(inp_compare(.false.,'do_cosmo_ks',field)) then
|
||||
do_cosmo_model=DO_COSMO_KS
|
||||
if (.not. rtdb_put(rtdb,'cosmo:do_cosmo_model',mt_int,1,
|
||||
$ do_cosmo_model))
|
||||
$ call errquit('cosmo_input: rtdb put failed',911, RTDB_ERR)
|
||||
cosmo_cavity=COSMO_CAVITY_SES
|
||||
if (.not.(rtdb_put(rtdb,'cosmo:do_cosmo_model',mt_int,1,
|
||||
$ do_cosmo_model)
|
||||
$ .and.rtdb_put(rtdb,'cosmo:cavity',mt_int,1,cosmo_cavity))
|
||||
$ ) call errquit('cosmo_input: rtdb put failed',911, RTDB_ERR)
|
||||
c
|
||||
c --- do_cosmo_yk: switch to York-Karplus model
|
||||
c --- do_cosmo_yk: switch to York-Karplus model; also makes cavity=vdw
|
||||
c
|
||||
else if(inp_compare(.false.,'do_cosmo_yk',field)) then
|
||||
do_cosmo_model=DO_COSMO_YK
|
||||
if (.not. rtdb_put(rtdb,'cosmo:do_cosmo_model',mt_int,1,
|
||||
$ do_cosmo_model))
|
||||
$ call errquit('cosmo_input: rtdb put failed',911, RTDB_ERR)
|
||||
cosmo_cavity=COSMO_CAVITY_VDW
|
||||
if (.not.(rtdb_put(rtdb,'cosmo:do_cosmo_model',mt_int,1,
|
||||
$ do_cosmo_model)
|
||||
$ .and.rtdb_put(rtdb,'cosmo:cavity',mt_int,1,cosmo_cavity)
|
||||
$ )) call errquit('cosmo_input: rtdb put failed',911, RTDB_ERR)
|
||||
c
|
||||
c --- do_cosmo_file flag
|
||||
c
|
||||
|
|
@ -333,8 +343,16 @@ c
|
|||
do_cosmo_file=.true.
|
||||
if (.not.
|
||||
$ rtdb_put(rtdb,'cosmo:do_cosmo_file',mt_log,1,do_cosmo_file))
|
||||
$ call errquit('cosmo_input: cannot put do_cosmo_file in rtdb',
|
||||
$ 0,rtdb_err)
|
||||
$ call errquit('cosmo_input: rtdb put failed',911, RTDB_ERR)
|
||||
c
|
||||
c --- info: Information line to be printed in the cosmo file as a comment.
|
||||
c Maximum lenth is 255 characters.
|
||||
c
|
||||
else if(inp_compare(.false.,'info',field)) then
|
||||
if (.not.inp_a(token))
|
||||
$ call errquit('cosmo_input: info',911, INPUT_ERR)
|
||||
if (.not.(rtdb_put(rtdb,'cosmo:info',mt_byte,255,token)))
|
||||
$ call errquit('cosmo_input: rtdb put failed',0,RTDB_ERR)
|
||||
c
|
||||
c --- rsolv: Used in Klamt-Schuurmann, but not in York-Karplus
|
||||
c --- approach
|
||||
|
|
@ -345,6 +363,84 @@ c
|
|||
if (.not. rtdb_put(rtdb,'cosmo:rsolv',mt_dbl,1,rsolv))
|
||||
$ call errquit('cosmo_input: rtdb put failed',911, RTDB_ERR)
|
||||
c
|
||||
c --- CAVITY: cavity construction method
|
||||
c CAVITY VDW : van der Waals cavity
|
||||
c CAVITY SES : solvent-excluded-cavity
|
||||
c
|
||||
c default for each model:
|
||||
c - CAVITY SES : with the Klamt-Schuurmann model
|
||||
c - CAVITY VDW : with the York-Karplus model
|
||||
c
|
||||
else if(inp_compare(.false.,'cavity',field)) then
|
||||
if (.not.inp_a(token))
|
||||
$ call errquit('cosmo_input: cavity',911, INPUT_ERR)
|
||||
if (inp_compare(.false.,'vdw',token)) then
|
||||
cosmo_cavity = COSMO_CAVITY_VDW
|
||||
else if (inp_compare(.false.,'ses',token)) then
|
||||
cosmo_cavity = COSMO_CAVITY_SES
|
||||
c use KS model by default when using SES cavity
|
||||
do_cosmo_model=DO_COSMO_KS
|
||||
c correct potential when using SES
|
||||
cosmo_ptcor=.true.
|
||||
else
|
||||
write(luout,*)"invalid option for CAVITY, valid options are:"
|
||||
write(luout,*)"- VDW for a van der Waals cavity"
|
||||
write(luout,*)"- SES for a solvent-excluded-cavity"
|
||||
call util_flush(luout)
|
||||
call errquit("cosmo_input: invalid option for CAVITY",911,
|
||||
$ INPUT_ERR)
|
||||
endif
|
||||
if (.not. rtdb_put(rtdb,'cosmo:cavity',mt_int,1,cosmo_cavity))
|
||||
$ call errquit('cosmo_input: rtdb put failed',911, RTDB_ERR)
|
||||
if (.not. rtdb_put(rtdb,'cosmo:do_cosmo_model',mt_int,1,
|
||||
C do_cosmo_model))
|
||||
$ call errquit('cosmo_input: rtdb put failed',912, RTDB_ERR)
|
||||
if (.not.
|
||||
$ rtdb_put(rtdb,'cosmo:ptcor',mt_log,1,cosmo_ptcor))
|
||||
$ call errquit('cosmo_input: rtdb put failed',913, RTDB_ERR)
|
||||
c
|
||||
c --- ndiv: specifies the division level for the triangles on
|
||||
c --- sphere surface when a SES cavity is used.
|
||||
c Valid values are:
|
||||
c - coarse: 60 triangles per sphere
|
||||
c - fine : 240 (default)
|
||||
c - xfine : 960
|
||||
c - huge : 3840
|
||||
c - xxl :15360
|
||||
c
|
||||
else if(inp_compare(.false.,'ndiv',field)) then
|
||||
if (.not.inp_a(token))
|
||||
$ call errquit('cosmo_input: ndiv',911, INPUT_ERR)
|
||||
if (inp_compare(.false.,'coarse',token)) then
|
||||
cosmo_ndiv = 1
|
||||
else if (inp_compare(.false.,'fine',token)) then
|
||||
cosmo_ndiv = 2
|
||||
else if (inp_compare(.false.,'xfine',token)) then
|
||||
cosmo_ndiv = 3
|
||||
else if (inp_compare(.false.,'huge',token)) then
|
||||
cosmo_ndiv = 4
|
||||
else if (inp_compare(.false.,'xxl',token)) then
|
||||
cosmo_ndiv = 5
|
||||
else
|
||||
write(luout,*)"invalid option for NDIV, valid options are:"
|
||||
write(luout,*)" coarse, fine (default), xfine"
|
||||
call util_flush(luout)
|
||||
call errquit("cosmo_input: invalid option for NDIV",911,
|
||||
$ INPUT_ERR)
|
||||
endif
|
||||
if (.not. rtdb_put(rtdb,'cosmo:ndiv',mt_int,1,cosmo_ndiv))
|
||||
$ call errquit('cosmo_input: rtdb put failed',911,RTDB_ERR)
|
||||
c
|
||||
c --- mfactor: Merging factor for segments that are too close.
|
||||
c Any two segments closer than f(rsolv,ndiv) * mfactor are merged into
|
||||
c a single segment. The default value is 1.0.
|
||||
c
|
||||
else if(inp_compare(.false.,'mfactor',field)) then
|
||||
if(.not. inp_f(mfactor))
|
||||
$ call errquit('cosmo_input: mfactor',911, INPUT_ERR)
|
||||
if (.not. rtdb_put(rtdb,'cosmo:mfactor',mt_dbl,1,mfactor))
|
||||
$ call errquit('cosmo_input: rtdb put failed',911, RTDB_ERR)
|
||||
c
|
||||
c --- parameter file
|
||||
c
|
||||
else if(inp_compare(.false.,'parameters',field)) then
|
||||
|
|
@ -481,6 +577,15 @@ c
|
|||
if (.not. rtdb_put(rtdb,'cosmo:sccor',mt_int,1,cosmo_sccor))
|
||||
$ call errquit('cosmo_input: rtdb put failed',911, RTDB_ERR)
|
||||
c
|
||||
c --- potcorr flag: use the potential
|
||||
c correction associated with charge corrections
|
||||
c
|
||||
else if(inp_compare(.false.,'potcorr',field)) then
|
||||
if (.not. inp_l(cosmo_ptcor)) cosmo_ptcor=.true.
|
||||
if (.not.
|
||||
$ rtdb_put(rtdb,'cosmo:ptcor',mt_log,1,cosmo_ptcor))
|
||||
$ call errquit('cosmo_input: rtdb put failed',911, RTDB_ERR)
|
||||
c
|
||||
c --- minbem
|
||||
c
|
||||
else if(inp_compare(.false.,'minbem',field)) then
|
||||
|
|
|
|||
|
|
@ -5,9 +5,10 @@ c
|
|||
double precision adiag,dsurf,dvol,srfmol,volmol,ptspatm
|
||||
integer do_cosmo_model,lineq,minbem,maxbem,ificos,ifscrn,
|
||||
& cosmo_sccor,iangleb,fibonacci,thomson
|
||||
logical cosmo_ptcor
|
||||
common/hnd_cospar/dielec,dielecinf,screen,rsolv,zeta,gammas,swtol
|
||||
common/hnd_cosmod/do_cosmo_model,lineq,minbem,maxbem,
|
||||
I ificos,ifscrn,
|
||||
& cosmo_sccor,iangleb,fibonacci,thomson
|
||||
& cosmo_ptcor,cosmo_sccor,iangleb,fibonacci,thomson
|
||||
common/hnd_cosdat/adiag,dsurf,dvol,srfmol,volmol,ptspatm
|
||||
|
||||
|
|
|
|||
2593
src/solvation/gepol_lib.F
Normal file
2593
src/solvation/gepol_lib.F
Normal file
File diff suppressed because it is too large
Load diff
|
|
@ -445,10 +445,22 @@ C> "Envelope theorems for arbitrary choice sets",
|
|||
C> <i>Econometrica</i> (2002) <b>70</b>, 583-601, DOI:
|
||||
C> <a href="https://doi.org/10.1111/1468-0262.00296">
|
||||
C> 10.1111/1468-0262.00296</a>.
|
||||
C>
|
||||
C> [10] A. Klamt, V. Jonas, T. Burger, J. C. W. Lohrenz,
|
||||
C> "Refinement and Parametrization of COSMO-RS",
|
||||
C> <i>J. Phys. Chem. A</i> (1998) <b>102</b>, 1089-5639, DOI:
|
||||
C> <a href="https://doi.org/10.1021/jp980017s">
|
||||
C> 10.1021/jp980017s</a>.
|
||||
C>
|
||||
C> [11] A. Klamt, V. Jonas,
|
||||
C> "Treatment of the outlying charge in continuum solvation models",
|
||||
C> <i>J. Chem. Phys.</i> (1996) <b>105</b>, pp 9972–9981, DOI:
|
||||
C> <a href="https://doi.org/10.1063/1.472829">
|
||||
C> 10.1063/1.472829</a>.
|
||||
C>
|
||||
subroutine hnd_coschg(g_dens,ndens,rtdb,geom,basis,nat,nefc,
|
||||
& efcc,efcs,msrf,efcz,efczz,efciat,ratm,
|
||||
& ecos,cosmo_file_in)
|
||||
& ecos,egas,esol,cosmo_file_in)
|
||||
implicit none
|
||||
#include "errquit.fh"
|
||||
#include "global.fh"
|
||||
|
|
@ -489,11 +501,15 @@ c
|
|||
double precision ratm(nat) !< [Input] the atom radii
|
||||
double precision ecos !< [Output] the energy contribution due to
|
||||
!< the COSMO charges
|
||||
double precision egas !< [Input] the total gas energy
|
||||
double precision esol !< [Input] the total solvated energy
|
||||
logical status
|
||||
logical do_cosmo_file
|
||||
integer cosmo_cavity
|
||||
c
|
||||
logical dbug,more,out,direct,noall,all,elec,nucl,iefc_done
|
||||
character*16 at_tag
|
||||
character*255 cosmo_info
|
||||
integer istrlen
|
||||
character*255 cosmo_file_in
|
||||
character*(nw_max_path_len) cosmo_file
|
||||
|
|
@ -528,13 +544,13 @@ c integer cosmo_sccor ! do correction?
|
|||
integer nodcmp ! flag specifying how to handle errors
|
||||
integer need ! the amount of memory needed
|
||||
c
|
||||
integer l_epot, l_xyzpt, l_zanpt ! memory handles
|
||||
integer k_epot, k_xyzpt, k_zanpt ! memory offsets
|
||||
integer l_epot, l_xyzpt, l_zanpt, l_costag ! memory handles
|
||||
integer k_epot, k_xyzpt, k_zanpt, k_costag ! memory offsets
|
||||
c
|
||||
double precision charge ! the total QM region charge
|
||||
double precision chgnuc ! the total nuclear charge
|
||||
integer nelec ! the total number of electrons
|
||||
double precision chgfac ! scale factor for COSMO charges
|
||||
double precision chgfac, chgfacn, chgface ! scale factor for COSMO charges
|
||||
double precision chgcos ! the total COSMO surface charge
|
||||
double precision chgcvg ! the convergence of the COSMO charges
|
||||
double precision chgina ! the inv(A) COSMO charge
|
||||
|
|
@ -556,7 +572,6 @@ c
|
|||
double precision solnrg ! solvation energy
|
||||
double precision dlambda ! lambda (surface charge correction)
|
||||
double precision elambda ! lambda dependent energy term
|
||||
double precision ecos2
|
||||
double precision pi
|
||||
double precision zero, pt5, one, two ! constants
|
||||
data zero /0.0d+00/
|
||||
|
|
@ -719,9 +734,11 @@ c
|
|||
& call errquit('hnd_coschg: ma failed',911,MA_ERR)
|
||||
if (.not. ma_push_get(mt_dbl,nat,'zan pnt',l_zanpt,k_zanpt))
|
||||
& call errquit('hnd_coschg: ma failed',911,MA_ERR)
|
||||
if (.not. ma_push_get(mt_byte,nat*16,'tags',l_costag,k_costag))
|
||||
& call errquit('hnd_coschg: k_costag failed',911,MA_ERR)
|
||||
do iat=1,nat
|
||||
if(.not.geom_cent_get(geom,iat,at_tag,dbl_mb(k_xyzpt+3*(iat-1)),
|
||||
& dbl_mb(k_zanpt+iat-1))) call
|
||||
if(.not.geom_cent_get(geom,iat,byte_mb(k_costag+16*(iat-1)),
|
||||
& dbl_mb(k_xyzpt+3*(iat-1)),dbl_mb(k_zanpt+iat-1))) call
|
||||
& errquit('hnd_coschg: geom_cent_get',911,GEOM_ERR)
|
||||
enddo ! iat
|
||||
c
|
||||
|
|
@ -1005,9 +1022,11 @@ c
|
|||
else if (nucl) then
|
||||
errcos=chgnuc-chgcos
|
||||
chgfac=chgnuc/chgcos
|
||||
chgfacn = chgfac
|
||||
else if (elec) then
|
||||
errcos=-dble(nelec)-chgcos
|
||||
chgfac=-dble(nelec)/chgcos
|
||||
chgface = chgfac
|
||||
endif
|
||||
call dscal(nefc,chgfac,dbl_mb(ieq),1)
|
||||
else if (cosmo_sccor.eq.COSMO_SCCOR_LAGRA) then
|
||||
|
|
@ -1042,6 +1061,23 @@ c
|
|||
enddo
|
||||
endif
|
||||
c
|
||||
c ----- update potentials due to outlying charge correction
|
||||
c
|
||||
if (cosmo_sccor.ne.COSMO_SCCOR_NO.and.cosmo_ptcor) then
|
||||
c If outlying charge corrections have been applied, the total
|
||||
c potential should be updated, pot = -A*q, see Eq. 12 of Ref. [11].
|
||||
c
|
||||
c The total potential is stored at i10, total point charges at i20.
|
||||
call hnd_cosaxd(nat,dbl_mb(i20),dbl_mb(i10),nefc,efcc,
|
||||
+ efcs,efczz,efciat,ratm)
|
||||
c The nuclear potential should not be changed by the outlying
|
||||
c charges, so the elec potential should be adjusted.
|
||||
c Elec potential (i12) = total (i10) - nuc (i11)
|
||||
do ief=1,nefc
|
||||
dbl_mb(ief+i12-1) = dbl_mb(ief+i10-1) - dbl_mb(ief+i11-1)
|
||||
enddo
|
||||
endif
|
||||
c
|
||||
c ----- charge screening due to the dielectric medium -----
|
||||
c
|
||||
c ----- set screening factor -----
|
||||
|
|
@ -1106,6 +1142,13 @@ c surface charge corrections are used the results should be
|
|||
c identical. If surface charge corrections are employed using
|
||||
c scaling factors or Lagrangian multipliers then additional
|
||||
c correction terms are needed to ensure the expressions agree.
|
||||
c
|
||||
c A consistent correction is to recalculate the total potential
|
||||
c with the corrected charges (see Ref. [11] and cosmo_ptcor above).
|
||||
c After that, adjust the elec potential accordingly, with a
|
||||
c constant nuclear potential. This makes both formulations
|
||||
c agree and also makes scale and Lagrangian corrections
|
||||
c to produce similar results, elambda must be disregarded.
|
||||
c
|
||||
call hnd_cos_energy(nat,nefc,chgfac,efcc,efcs,efcz,efczz,efciat,
|
||||
& ratm,dbl_mb(k_xyzpt),dbl_mb(k_zanpt),
|
||||
|
|
@ -1131,22 +1174,22 @@ c
|
|||
allefc = ddot(nefc,efcz,1,dbl_mb(i10),1)
|
||||
atmefc = ddot(nefc,efcz,1,dbl_mb(i11),1)
|
||||
elcefc = ddot(nefc,efcz,1,dbl_mb(i12),1)
|
||||
solnrg= pt5* allefc + elambda
|
||||
c solnrg= pt5* allefc + elambda
|
||||
solnrg = pt5*allefc
|
||||
ecos = pt5*(atmefc-elcefc)
|
||||
c COSMO contribution Alternative 2 (Ref.[1] Eq.(11))
|
||||
c ecos = pt5*(atmefc-elcefc)+elambda
|
||||
if (do_cosmo_smd) then
|
||||
ecos = pt5*(atmefc-elcefc)
|
||||
else
|
||||
c ecos = efcefc + atmefc
|
||||
ecos = pt5*(atmefc-elcefc) + elambda
|
||||
endif
|
||||
c add lagrangian multiplier correction to the energy
|
||||
c when the potential is not corrected
|
||||
c
|
||||
if(.not.cosmo_ptcor) ecos=ecos+elambda
|
||||
|
||||
if (oprint_energies) then
|
||||
write(luout,*)'Alternative 2'
|
||||
write(luout,9991) atmefc
|
||||
write(luout,9990) elcefc
|
||||
write(luout,9989) allefc
|
||||
write(luout,9988) solnrg
|
||||
write(luout,9989) allefc
|
||||
write(luout,9994) ecos
|
||||
endif
|
||||
|
||||
|
|
@ -1223,6 +1266,8 @@ c
|
|||
if (.not. rtdb_get(rtdb,'cosmo:do_cosmo_file',mt_log,1,
|
||||
$ do_cosmo_file)) do_cosmo_file=.false.
|
||||
if (do_cosmo_file) then
|
||||
if (.not. rtdb_get(rtdb,'cosmo:cavity',mt_int,1,
|
||||
$ cosmo_cavity)) cosmo_cavity=COSMO_CAVITY_VDW
|
||||
cosmo_file_in = "cosmo"
|
||||
call util_file_name(cosmo_file_in,.false.,.false.,cosmo_file)
|
||||
call util_file_name_resolve(cosmo_file,.false.)
|
||||
|
|
@ -1235,37 +1280,78 @@ c
|
|||
write(*,*) "printing cosmo file for COSMO-RS/SAC",
|
||||
+ cosmo_file
|
||||
end if
|
||||
if (rtdb_get(rtdb,'cosmo:info',mt_byte,255,cosmo_info))
|
||||
+ write(fn,"(a)") '# ' // trim(cosmo_info)
|
||||
write(fn,"(a)") "$cosmo"
|
||||
write(fn,*) " epsilon= ", dielec
|
||||
write(fn,*) " rsolv= ", rsolv
|
||||
write(fn,"(a,f6.3)") " screen= ", screen
|
||||
if(screen.eq.one) then
|
||||
write(fn,*) " epsilon= infinity"
|
||||
else
|
||||
write(fn,"(a,f6.3)") " epsilon= ", dielec
|
||||
endif
|
||||
if(cosmo_cavity.eq.COSMO_CAVITY_SES) then
|
||||
write(fn,*) " cavity= SES"
|
||||
write(fn,"(a,f6.3)") " rsolv= ", rsolv
|
||||
else
|
||||
write(fn,*) " cavity= vdW"
|
||||
endif
|
||||
if(do_cosmo_model.eq.DO_COSMO_YK) then
|
||||
write(fn,*) " model= YK"
|
||||
write(fn,"(a,f6.3)") " zeta= ", zeta
|
||||
else
|
||||
write(fn,*) " model= KS"
|
||||
endif
|
||||
if (cosmo_sccor.eq.COSMO_SCCOR_NO) then
|
||||
write(fn,*) " charge_correction= no"
|
||||
else if (cosmo_sccor.eq.COSMO_SCCOR_LAGRA) then
|
||||
write(fn,*) " charge_correction= lagrangian"
|
||||
else if (cosmo_sccor.eq.COSMO_SCCOR_SCALE) then
|
||||
write(fn,*) " charge_correction= scale"
|
||||
write(fn,"(a,f12.9)") " charge_corr_elec= ", chgface
|
||||
write(fn,"(a,f12.9)") " charge_corr_nucl= ", chgfacn
|
||||
end if
|
||||
c
|
||||
write(fn,"(a)") "$cosmo_data"
|
||||
write(fn,*) " nps= ", nefc
|
||||
write(fn,*) " area= ", srfmol/(cau2ang**2)
|
||||
write(fn,*) " volume= ", volmol/(cau2ang**3)
|
||||
write(fn,"(a,i6)") " nps= ", nefc
|
||||
write(fn,"(a,f10.2)") " area= ", srfmol/(cau2ang**2)
|
||||
write(fn,"(a,f10.2)") " volume= ", volmol/(cau2ang**3)
|
||||
c
|
||||
write(fn,"(a)") "$coord_rad"
|
||||
write(fn,"(a)") "#atom x y z [a.u.] element radius [A]"
|
||||
do i = 1,nat
|
||||
write(fn,*) i,
|
||||
call util_set_ma_char_arrays(16,
|
||||
+ byte_mb(k_costag+16*(i-1)),at_tag)
|
||||
write(fn,"(i6,3f15.9,2x,a,f6.3)") i,
|
||||
+ dbl_mb(k_xyzpt +3*(i-1)),
|
||||
+ dbl_mb(k_xyzpt+1+3*(i-1)),
|
||||
+ dbl_mb(k_xyzpt+2+3*(i-1)),
|
||||
+ int(dbl_mb(k_zanpt+i-1)),
|
||||
+ at_tag,
|
||||
+ ratm(i)*cau2ang
|
||||
enddo ! i
|
||||
c
|
||||
c
|
||||
write(fn,"(a)") "$energy"
|
||||
if(dabs(egas).gt.0d0)
|
||||
+ write(fn,"(a,f18.10)") " total_gas= ", egas
|
||||
if(dabs(esol).gt.0d0)
|
||||
+ write(fn,"(a,f18.10)") " total_solvated= ", esol
|
||||
c
|
||||
c Dielectric energy = 0.5 * sum(potential_i * q_i), Eq. (5) of Ref. [10].
|
||||
c This energy is expected to correlate well with the solvation energy.
|
||||
write(fn,"(a,f18.10)") " diel= ", pt5*allefc
|
||||
c
|
||||
write(fn,"(a)") "$segment_information"
|
||||
write(fn,"(a)") "# n atom x y z charge area charge/area"
|
||||
write(fn,"(a)") "# coordinates [a.u.], area [A2]"
|
||||
write(fn,"(a)")
|
||||
+ "# n atom x y z charge area charge/area potential"
|
||||
write(fn,"(a)")
|
||||
+ "# coordinates and potential [a.u.], area [A2]"
|
||||
do ief=1,nefc
|
||||
efcsi = efcs(ief)*(cau2ang**2)
|
||||
if (do_cosmo_model.eq.DO_COSMO_YK)
|
||||
+ efcsi = msrf(ief)*(cau2ang**2)
|
||||
|
||||
write(fn,*) ief, efciat(ief),
|
||||
write(fn,"(2i6,7f15.9)") ief, efciat(ief),
|
||||
+ efcc(1,ief), efcc(2,ief), efcc(3,ief),
|
||||
+ efcz(ief), efcsi, efcz(ief)/efcsi
|
||||
+ efcz(ief), efcsi, efcz(ief)/efcsi,
|
||||
+ dbl_mb(i10+ief-1)
|
||||
end do
|
||||
close(fn)
|
||||
end if
|
||||
|
|
|
|||
|
|
@ -190,6 +190,8 @@ c
|
|||
double precision wleb(mxfac)
|
||||
double precision energy
|
||||
c
|
||||
integer cosmo_cavity
|
||||
double precision mfactor
|
||||
logical oprint_out
|
||||
logical oprint_more
|
||||
logical oprint_debug
|
||||
|
|
@ -204,6 +206,11 @@ c
|
|||
D (ga_nodeid().eq.0)
|
||||
oprint_more = util_print("cosmo_cossrf_more",print_never).and.
|
||||
D (ga_nodeid().eq.0)
|
||||
c
|
||||
if (.not. rtdb_get(rtdb,'cosmo:cavity',mt_int,1,
|
||||
$ cosmo_cavity)) cosmo_cavity=COSMO_CAVITY_VDW
|
||||
if (.not. rtdb_get(rtdb,'cosmo:mfactor',mt_dbl,1,
|
||||
$ mfactor)) mfactor=1.d0
|
||||
c
|
||||
c ----- approximate sphere with segments and points -----
|
||||
c
|
||||
|
|
@ -267,7 +274,8 @@ c
|
|||
if(radius(iat).eq.0.0d0) then
|
||||
ratm(iat)=0.0d0
|
||||
else
|
||||
if (do_cosmo_model.eq.DO_COSMO_KS) then
|
||||
if (do_cosmo_model.eq.DO_COSMO_KS.and.
|
||||
+ cosmo_cavity.ne.COSMO_CAVITY_SES) then
|
||||
ratm(iat)=(radius(iat)+rsolv)/cau2ang
|
||||
else
|
||||
ratm(iat)=radius(iat)/cau2ang
|
||||
|
|
@ -280,8 +288,8 @@ c
|
|||
|
||||
call hnd_cossas(nat,xyzatm,ratm,mxatm,
|
||||
1 nspa,nppa,xyzspa,ijkspa,
|
||||
2 nseg,nfac,xyzseg,ijkseg,insseg,
|
||||
3 numpps,xyzff,wleb,mxfac,geom,rtdb)
|
||||
2 nseg,nfac,xyzseg,ijkseg,insseg,numpps,
|
||||
3 xyzff,wleb,mxfac,geom,cosmo_cavity,mfactor,rtdb)
|
||||
c
|
||||
return
|
||||
9999 format(' nseg,nfac,ndiv=nfac/nseg,dsurf,dvol = ',3i7,2f10.6)
|
||||
|
|
@ -373,9 +381,9 @@ C> 10.1021/jp992097l</a>.
|
|||
C>
|
||||
subroutine hnd_cossas(nat,xyzatm,ratm,mxatom,
|
||||
1 nspa,nppa,xyzspa,ijkspa,
|
||||
2 nseg,nfac,xyzseg,ijkseg,insseg,
|
||||
3 numpps,xyzff,wleb,mxface,geom,
|
||||
4 rtdb)
|
||||
2 nseg,nfac,xyzseg,ijkseg,insseg,numpps,
|
||||
3 xyzff,wleb,mxface,geom,cosmo_cavity,
|
||||
4 mfactor,rtdb)
|
||||
implicit none
|
||||
#include "cosmo_params.fh"
|
||||
#include "errquit.fh"
|
||||
|
|
@ -424,15 +432,24 @@ c
|
|||
integer numpps( mxface,mxatom)
|
||||
double precision xyzff( mxface,mxatom)
|
||||
double precision wleb( mxface)
|
||||
double precision zero, one
|
||||
data one /1.0d+00/
|
||||
double precision zero, one, two
|
||||
data zero/0.0d00/,one/1.0d00/,two/2.0d00/
|
||||
integer l_efcc, k_efcc, l_efcs, k_efcs, l_efcz, k_efcz
|
||||
integer l_efclb, k_efclb, k_efciat, l_efciat
|
||||
integer l_efczz, k_efczz
|
||||
integer l_msrf,k_msrf
|
||||
c SES variables
|
||||
integer cosmo_cavity
|
||||
double precision mfactor, asum, dmin
|
||||
real*4 ofac,rd,dvec,rmim
|
||||
INTEGER*4 ndiv, gseg
|
||||
double precision segarea(mxface)
|
||||
integer segatom(mxface)
|
||||
double precision garea, gvolume
|
||||
c
|
||||
double precision ratm_real,dij,dum,cavdsp,pi,zetai,zetaii
|
||||
integer m,mfac,mseg
|
||||
integer nefc,iat,jat,npp,i,iseg,ifac,ief,ipp
|
||||
integer nefc,iat,jat,npp,i,iseg,jseg,ifac,ief,ipp
|
||||
|
||||
integer l_dum1, l_dum2, l_attag, k_dum1, k_dum2, k_attag
|
||||
character(len=16) aname
|
||||
|
|
@ -470,12 +487,22 @@ c
|
|||
c
|
||||
oprint_debug = util_print("cosmo_cossas_debug",print_debug).and.
|
||||
D (ga_nodeid().eq.0)
|
||||
dbug=oprint_debug
|
||||
oprint_molsurf = util_print("cosmo_mol_surface",print_never).and.
|
||||
D (ga_nodeid().eq.0)
|
||||
pi = acos(-1.0d0)
|
||||
c
|
||||
if(ga_nodeid().eq.0) then
|
||||
write(luout,9999)
|
||||
if(cosmo_cavity.eq.COSMO_CAVITY_SES) then
|
||||
write(luout,8888)
|
||||
else
|
||||
c YK model is currently using a vdW surface and not a SAS
|
||||
c as described in the original paper.
|
||||
c The KS model with a vdW cavity has a defect: it produces an
|
||||
c incomplete vdW surface, leaving solvent-excluded areas
|
||||
c open, small values of rsolv are needed.
|
||||
write(luout,9999)
|
||||
endif
|
||||
endif
|
||||
c
|
||||
c ----- print atomic centers -----
|
||||
|
|
@ -483,11 +510,12 @@ c
|
|||
if(ga_nodeid().eq.0) then
|
||||
write(luout,9998)
|
||||
do iat=1,nat
|
||||
if (do_cosmo_model.eq.DO_COSMO_KS) then
|
||||
if (do_cosmo_model.eq.DO_COSMO_KS.and.
|
||||
+ cosmo_cavity.ne.COSMO_CAVITY_SES) then
|
||||
write(luout,9997) iat,xyzatm(1,iat),xyzatm(2,iat),
|
||||
1 xyzatm(3,iat),
|
||||
2 (ratm(iat)*cau2ang-rsolv)
|
||||
else if (do_cosmo_model.eq.DO_COSMO_YK) then
|
||||
else
|
||||
write(luout,9997) iat,xyzatm(1,iat),xyzatm(2,iat),
|
||||
1 xyzatm(3,iat),
|
||||
2 (ratm(iat)*cau2ang)
|
||||
|
|
@ -669,7 +697,7 @@ c
|
|||
c
|
||||
enddo
|
||||
c
|
||||
if(ga_nodeid().eq.0) then
|
||||
if(ga_nodeid().eq.0.and.cosmo_cavity.ne.COSMO_CAVITY_SES) then
|
||||
write(luout,9985) nseg,nfac
|
||||
write(luout,9992)
|
||||
do iat=1,nat
|
||||
|
|
@ -680,7 +708,7 @@ c
|
|||
write(luout,9991) iat,nspa(iat),nppa(iat),npp
|
||||
enddo
|
||||
endif
|
||||
if(oprint_debug) then
|
||||
if(oprint_debug.and.cosmo_cavity.ne.COSMO_CAVITY_SES) then
|
||||
write(luout,9987)
|
||||
do iat=1,nat
|
||||
do iseg=1,nseg
|
||||
|
|
@ -701,6 +729,25 @@ c
|
|||
endif
|
||||
enddo
|
||||
c
|
||||
c Construct a precise SES surface, using a modified GEPOL93.
|
||||
c
|
||||
if (cosmo_cavity.eq.COSMO_CAVITY_SES) then
|
||||
c We are sending all arguments in A.U.
|
||||
rd = rsolv/cau2ang
|
||||
rmim = rd/2
|
||||
ofac = 0.9 ! to reduce the concave regions
|
||||
dvec = 1.0 ! segment vector direction, not relevant
|
||||
if(.not.rtdb_get(rtdb,'cosmo:ndiv',mt_int,1,ndiv)) ndiv=2
|
||||
call gepol('ESURF',.false.,.false.,.false.,.false.,'TIT',0,
|
||||
& rmim,'','','',ofac,rd,ndiv,dvec,
|
||||
& .true.,.false.,
|
||||
& nat,ratm,xyzatm,mxface,
|
||||
& gseg,xyzseg,segarea,segatom,srfmol,volmol,.false.)
|
||||
nefc = gseg
|
||||
nseg = gseg
|
||||
end if
|
||||
c
|
||||
c
|
||||
c Allocate memory for point charges
|
||||
c
|
||||
if(.not.ma_push_get(mt_dbl,nefc*3,'cosmo efcc',l_efcc,k_efcc))
|
||||
|
|
@ -736,6 +783,72 @@ c ----- save coordinates of surface points -----
|
|||
c save segment surfaces
|
||||
c save segment to atom mapping
|
||||
c
|
||||
if(cosmo_cavity.eq.COSMO_CAVITY_SES) then
|
||||
c Save gepol results, but keep the segments sorted by atom
|
||||
c so grad_hdn_cos can work properly.
|
||||
c
|
||||
c The minimum distance we will accept between 2 segments,
|
||||
c this is slight lower than the minimum distance for a rsolv sphere.
|
||||
dmin = rsolv/cau2ang * 0.3 * mfactor
|
||||
if (ndiv.eq.2) dmin = dmin/2.0
|
||||
if (ndiv.ge.3) dmin = dmin/4.0
|
||||
c
|
||||
c Checking for overlapping segments to merge.
|
||||
if (do_cosmo_model.ne.DO_COSMO_YK.and.
|
||||
A dmin.gt.zero) then
|
||||
iseg = 0
|
||||
do while (iseg <= nseg)
|
||||
iseg = iseg + 1
|
||||
if(segarea(iseg).le.zero) cycle
|
||||
do jseg=iseg+1,nseg
|
||||
if(segarea(jseg).le.zero) cycle
|
||||
dij=dist(
|
||||
I xyzseg(1,iseg),xyzseg(2,iseg),xyzseg(3,iseg),
|
||||
J xyzseg(1,jseg),xyzseg(2,jseg),xyzseg(3,jseg))
|
||||
if(dij.lt.dmin) then
|
||||
c Accumulate the area at the centroid.
|
||||
asum = segarea(iseg) + segarea(jseg)
|
||||
do m=1,3
|
||||
xyzseg(m,iseg) = (segarea(iseg)*xyzseg(m,iseg)+
|
||||
+ segarea(jseg)*xyzseg(m,jseg))/asum
|
||||
end do
|
||||
segarea(iseg) = asum;
|
||||
segarea(jseg) = zero;
|
||||
c Start over, perhaps 3 or more segments should be merged
|
||||
iseg = 0
|
||||
exit
|
||||
end if
|
||||
end do
|
||||
end do
|
||||
endif
|
||||
c Add the segments sorted by atom.
|
||||
ief = 0
|
||||
do iat=1,nat
|
||||
do iseg=1,nseg
|
||||
if(iat.ne.segatom(iseg).or.segarea(iseg).le.zero) cycle
|
||||
c
|
||||
ief = ief+1
|
||||
dbl_mb(k_efcc+3*(ief-1)) =xyzseg(1,iseg)
|
||||
dbl_mb(k_efcc+3*(ief-1)+1)=xyzseg(2,iseg)
|
||||
dbl_mb(k_efcc+3*(ief-1)+2)=xyzseg(3,iseg)
|
||||
|
||||
dbl_mb(k_efcs+ief-1) = segarea(iseg) ! KS area
|
||||
if (do_cosmo_model.eq.DO_COSMO_YK) then
|
||||
c Store the YK variables.
|
||||
zetai=zeta/sqrt(segarea(iseg)) ! zetai=zeta/sqrt(dsurf)/ratm_real
|
||||
zetaii=zetai*sqrt(2d0/pi)
|
||||
xyzff(iseg,iat) = one ! no segments inside other spheres
|
||||
dbl_mb(k_efcs+ief-1) = zetaii ! zetaii/xyzff(iseg,iat))
|
||||
dbl_mb(k_msrf+ief-1) = segarea(iseg) ! YK area
|
||||
dbl_mb(k_efczz+ief-1) = zetai
|
||||
end if
|
||||
c Atom map.
|
||||
int_mb(k_efciat+ief-1) = iat
|
||||
enddo
|
||||
enddo
|
||||
nefc = ief
|
||||
nseg = nefc
|
||||
else
|
||||
srfmol=0d0
|
||||
volmol=0d0
|
||||
ief =0
|
||||
|
|
@ -805,6 +918,24 @@ c 775
|
|||
enddo
|
||||
endif
|
||||
enddo
|
||||
c Volume is underestimated with the above method, let's use GEPOL
|
||||
c just to get a better volume estimate for the vdW cavity.
|
||||
c For the KS method the SES cavity should be used.
|
||||
if (do_cosmo_model.eq.DO_COSMO_YK) then
|
||||
rd = 0! no solvent
|
||||
rmim = rd/2! dummy, not used
|
||||
ofac = 0.9 ! dummy, not used
|
||||
dvec = 1.0 ! segment vector direction, not relevant
|
||||
ndiv = 1
|
||||
call gepol('WSURF',.false.,.false.,.false.,.false.,'TIT',0,
|
||||
& rmim,'','','',ofac,rd,ndiv,dvec,
|
||||
& .true.,.false.,nat,ratm,xyzatm,mxface,
|
||||
& gseg,xyzseg,segarea,segatom,
|
||||
& garea,gvolume,.false.)
|
||||
volmol = gvolume
|
||||
endif
|
||||
c
|
||||
endif
|
||||
srfmol=srfmol*(cau2ang**2)
|
||||
volmol=volmol*(cau2ang**3)
|
||||
c
|
||||
|
|
@ -928,7 +1059,8 @@ c
|
|||
& errquit('cosmo_cossas chop stack k_efcc failed',911,MA_ERR)
|
||||
c
|
||||
return
|
||||
9999 format(/,1x,'solvent accessible surface',/,1x,26(1h-))
|
||||
9999 format(/,1x,' van der Waals surface ',/,1x,26(1h-))
|
||||
8888 format(/,1x,' solvent excluded surface ',/,1x,26(1h-))
|
||||
9998 format(/,1x,'---------- ATOMIC COORDINATES (A.U.) ----------',
|
||||
1 '-- VDWR(ANG.) --')
|
||||
9997 format( 1x,i5,3f14.8,f10.3)
|
||||
|
|
@ -1794,13 +1926,13 @@ c
|
|||
c
|
||||
double precision allefc !< [Output] The total solute charge
|
||||
!< density - COSMO charge interaction
|
||||
!< energy
|
||||
!< energy (pot*q)
|
||||
double precision atmefc !< [Output] The nuclear - COSMO charge
|
||||
!< interaction energy
|
||||
!< interaction energy (Q*B*q)
|
||||
double precision elcefc !< [Output] The electron - COSMO charge
|
||||
!< interaction energy
|
||||
double precision efcefc !< [Output] The COSMO charge - COSMO
|
||||
!< charge interaction energy
|
||||
!< charge interaction energy (q'*A*q/2)
|
||||
c
|
||||
c
|
||||
integer ief, jef !< Counters over COSMO charges
|
||||
|
|
|
|||
|
|
@ -40,20 +40,24 @@ c
|
|||
integer ibegin,iend,ilen,i
|
||||
character*4096 newchr
|
||||
integer maxno_authors,len_newchr
|
||||
parameter(maxno_authors=107)
|
||||
parameter(maxno_authors=108)
|
||||
character*64 name_author(maxno_authors)
|
||||
data name_author/
|
||||
+ 'E. Apra', 'E. J. Bylaska',
|
||||
+ 'N. Govind', 'K. Kowalski',
|
||||
+ 'D. Mejia-Rodriguez',
|
||||
+ 'N. P. Bauman', 'A. Panyala',
|
||||
+ 'R. J. Harrison',
|
||||
+ 'M. Valiev',
|
||||
+ 'D. Mejia-Rodriguez', 'A. Kunitsa',
|
||||
+ 'N. P. Bauman', 'A. Panyala',
|
||||
+ 'W. A. de Jong', 'T. P. Straatsma', 'H. J. J. van Dam',
|
||||
+ 'D. Wang', 'T. L. Windus',
|
||||
+ 'J. Hammond', 'J. Autschbach','A. Woods',
|
||||
+ 'J. Hammond', 'J. Autschbach',
|
||||
+ 'R. de P. Soares',
|
||||
+ 'A. Kunitsa',
|
||||
+ 'K. Bhaskaran-Nair',
|
||||
+ 'J. Brabec','K. Lopata','S. A. Fischer','S. Krishnamoorthy',
|
||||
+ 'M. Jacquelin',
|
||||
+ 'A. Woods',
|
||||
+ 'W. Ma', 'M. Klemm', 'O. Villa', 'Y. Chen', 'V. Anisimov',
|
||||
+ 'F. Aquino', 'S. Hirata', 'M. T. Hackler',
|
||||
+ 'E. Hermes', 'L. Jensen', 'J. E. Moore', 'J. C. Becca',
|
||||
|
|
@ -61,7 +65,7 @@ c
|
|||
+ 'M. Malagoli', 'A. Marenich', 'A. Otero-de-la-Roza',
|
||||
+ 'J. Mullin', 'P. Nichols', 'R. Peverati', 'J. Pittner',
|
||||
+ 'Y. Zhao', 'P.-D. Fan', 'A. Fonari', 'M. J. Williamson',
|
||||
+ 'R. J. Harrison', 'J. R. Rehr',
|
||||
+ 'J. R. Rehr',
|
||||
+ 'M. Dupuis', 'D. Silverstein', 'D. M. A. Smith',
|
||||
+ 'J. Nieplocha', 'V. Tipparaju', 'M. Krishnan',
|
||||
+ 'B. E. Van Kuiken', 'A. Vazquez-Mayagoitia',
|
||||
|
|
|
|||
|
|
@ -124,6 +124,7 @@ fi
|
|||
fi
|
||||
if [[ ! $(grep -i cosmo $TRAVIS_BUILD_DIR/src/stubs.F| awk '/cosmo_input/') ]]; then
|
||||
cd $TRAVIS_BUILD_DIR/QA && ./runtests.mpi.unix procs $nprocs cosmo_h2o_dft
|
||||
cd $TRAVIS_BUILD_DIR/QA && ./runtests.mpi.unix procs $nprocs cosmo_h2cco2_opt
|
||||
fi
|
||||
if [[ ! $(grep -i gw $TRAVIS_BUILD_DIR/src/stubs.F| awk '/gw_input/') ]]; then
|
||||
cd $TRAVIS_BUILD_DIR/QA && ./runtests.mpi.unix procs $nprocs ritddft_h2o ritddft_co
|
||||
|
|
|
|||
Loading…
Add table
Add a link
Reference in a new issue