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5.1 updates...EJB
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Eric Bylaska
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commit
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1 changed files with 471 additions and 5 deletions
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@ -1,5 +1,5 @@
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%
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% $Id: pspw.tex,v 1.42 2006-09-28 19:48:08 bylaska Exp $
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% $Id: pspw.tex,v 1.43 2007-12-21 18:48:11 bylaska Exp $
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%
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\label{sec:pspw}
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@ -118,6 +118,7 @@ PSPW
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TIME_STEP <real time_step default 5.8>
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LOOP <integer inner_iteration outer_iteration default 10 100>
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TOLERANCES <real tole tolc default 1.0e-7 1.0e-7>
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CUTOFF <real cutoff>
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ENERGY_CUTOFF <real ecut default (see input description)>
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WAVEFUNCTION_CUTOFF <real wcut default (see input description)>
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EWALD_NCUT <integer ncut default 1>]
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@ -170,7 +171,10 @@ The following list describes the keywords contained in the PSPW input block.
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\item $<$outer\_iteration$>$ - number of outer iterations
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\item $<$tole$>$ - value for the energy tolerance.
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\item $<$tolc$>$ - value for the one-electron orbital tolerance.
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\item $<$edit$>$ - value for the cutoff energy used
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\item $<$cutoff$>$ - value for the cutoff energy used to define the wavefunction. In addition
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using the CUTOFF keyword automatically sets the cutoff energy for the density
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to be twice the wavefunction cutoff.
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\item $<$ecut$>$ - value for the cutoff energy used
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to define the density. Default is set
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to be the maximum value that will fit
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within the simulation\_cell $<$cell\_name$>$.
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@ -765,6 +769,117 @@ center of mass shifting. This can be done by the following \verb+SET+ directive.
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set nwpw:com_shift .false.
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\end{verbatim}
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\subsection{\tt QM/MM}
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\label{sec:pspw_qmmm}
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A preliminary QM/MM capability that can run Car-Parrinello molecular dynamics has been integrated
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into the PSPW module. Currently, the input is not very robust but it is straightforward. The first
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step to run a QM/MM simulations is to define the MM atoms in the geometry block. The MM atoms must be
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at the end of the geometry and a carat, " \^\ ", must be appended to the end of the atom name, e.g.
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\begin{verbatim}
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geometry units angstrom nocenter noautosym noautoz print xyz
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C -0.000283 0.000106 0.000047
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Cl -0.868403 1.549888 0.254229
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Cl 0.834043 -0.474413 1.517103
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Cl -1.175480 -1.275747 -0.460606
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Cl 1.209940 0.200235 -1.310743
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O^ 0.3226E+01 -0.4419E+01 -0.5952E+01
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H^ 0.3193E+01 -0.4836E+01 -0.5043E+01
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H^ 0.4167E+01 -0.4428E+01 -0.6289E+01
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O^ 0.5318E+01 -0.3334E+01 -0.1220E+01
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H^ 0.4978E+01 -0.3040E+01 -0.2113E+01
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H^ 0.5654E+01 -0.2540E+01 -0.7127E+00
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end
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\end{verbatim}
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Next the pseudopotentials have be defined for the every type of MM atom contained in the geometry blocks. The
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following local pseudopotential suggested by Laio, VandeVondele and Rothlisberger can be automatically generated.
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\begin{eqnarray}
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V(\vec{r}) = -Z_{ion}\frac{{r_c}^{n_{\sigma}} - r^{n_{\sigma}}}{-sign(Z_{ion})*{r_c}^{n_{\sigma}+1}-r^{n_{\sigma}+1}}
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\end{eqnarray}
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The following input To define this pseudopo the O\^\ MM atom using the following input
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\begin{verbatim}
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NWPW
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QMMM
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mm_psp O^ -0.8476 4 0.70
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END
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END
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\end{verbatim}
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defines the local pseudopotential for the O\^\ MM atom , where $Z_{ion}=-0.8476$, $n_{\sigma}=4$, and $r_c=0.7$.
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The following input can be used to define the local pseudopotentials for all the MM atoms in the geometry
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block defined above
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\begin{verbatim}
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NWPW
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QMMM
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mm_psp O^ -0.8476 4 0.70
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mm_psp H^ 0.4238 4 0.40
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END
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END
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\end{verbatim}
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Next the Lenard-Jones potentials for the QM and MM atoms need to be defined. This is done as as follows
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\begin{verbatim}
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NWPW
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QMMM
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lj_ion_parameters C 3.41000000d0 0.10d0
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lj_ion_parameters Cl 3.45000000d0 0.16d0
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lj_ion_parameters O^ 3.16555789d0 0.15539425d0
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END
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END
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\end{verbatim}
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Note that the Lenard-Jones potential is not defined for the MM H atoms in this example.
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The final step is to define the MM fragments in the simulation. MM fragments are a set of
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atoms in which bonds and angle harmonic potentials are defined, or alternatively shake constraints are defined.
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The following input defines the fragments for the two water molecules in the above geometry,
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\begin{verbatim}
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NWPW
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QMMM
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fragment spc
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size 3 #size of fragment
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index_start 6:9:3 #atom index list that defines the start of
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# the fragments (start:final:stride)
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bond_spring 1 2 0.467307856 1.889726878 #bond i j Kspring r0
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bond_spring 1 3 0.467307856 1.889726878 #bond i j Kspring r0
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angle_spring 2 1 3 0.07293966 1.910611932 #angle i j k Kspring theta0
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end
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END
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END
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\end{verbatim}
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The fragments can be defined using shake constraints as
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\begin{verbatim}
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NWPW
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QMMM
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fragment spc
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size 3 #size of fragment
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index_start 6:9:3 #atom index list that defines the start of
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# the fragments (start:final:stride)
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shake units angstroms 1 2 3 cyclic 1.0 1.632993125 1.0
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end
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END
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END
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\end{verbatim}
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Alternatively, each water could be defined independently as follows.
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\begin{verbatim}
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NWPW
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QMMM
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fragment spc1
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size 3 #size of fragment
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index_start 6 #atom index list that defines the start of
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#the fragments
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bond_spring 1 2 0.467307856 1.889726878 #bond i j Kspring r0
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bond_spring 1 3 0.467307856 1.889726878 #bond i j Kspring r0
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angle_spring 2 1 3 0.07293966 1.910611932 #angle i j k Kspring theta0
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end
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fragment spc2
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size 3 #size of fragment
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index_start 9 #atom index list that defines the start of
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#the fragments
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shake units angstroms 1 2 3 cyclic 1.0 1.632993125 1.0
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end
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END
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END
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\end{verbatim}
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\subsection{\tt PSP\_GENERATOR}
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@ -1268,6 +1383,7 @@ NWPW
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TIME_STEP <real time_step default 5.8>
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LOOP <integer inner_iteration outer_iteration default 10 100>
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TOLERANCES <real tole tolc default 1.0e-7 1.0e-7>
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CUTOFF <real cutoff>
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ENERGY_CUTOFF <real ecut default (see input description)>
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WAVEFUNCTION_CUTOFF <real wcut default (see input description)>
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EWALD_NCUT <integer ncut default 1>]
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@ -1283,6 +1399,8 @@ NWPW
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BAND_DPLOT ... (see input description) END
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MAPPING <integer mapping default 1>
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SMEAR <sigma default 0.001> [TEMPERATURE <temperature>] [FERMI || GAUSSIAN default FERMI]
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[ORBITALS <integer orbitals default 4>]
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END
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\end{verbatim}
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@ -1305,6 +1423,9 @@ The following list describes these keywords.
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\item $<$outer\_iteration$>$ - number of outer iterations
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\item $<$tole$>$ - value for the energy tolerance.
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\item $<$tolc$>$ - value for the one-electron orbital tolerance.
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\item $<$cutoff$>$ - value for the cutoff energy used to define the wavefunction. In addition
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using the CUTOFF keyword automatically sets the cutoff energy for the density
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to be twice the wavefunction cutoff.
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\item $<$ecut$>$ - value for the cutoff energy used
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to define the density. Default is set
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to be the maximum value that will fit
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@ -1329,6 +1450,8 @@ The following list describes these keywords.
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\item BRILLOUIN\_ZONE (see section \ref{sec:band_brillouin_zone})
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\item MONKHORST-PACK - Alternatively, the MONKHORST-PACK keyword can be used
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to enter a MONKHORST-PACK sampling of the Brillouin zone.
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\item $<$smear$>$ - value for smearing broadending
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\item $<$temperature$>$ - same as smear but in units of K.
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\end{itemize}
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@ -1438,7 +1561,19 @@ This sub-directive specifies the molecular orbital number that is to be plotted.
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\end{verbatim}
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By default the grid spacing and the limits of the cell to be plotted are defined by the input wavefunctions. Alternatively the user can use the LIMITXYZ sub-directive to specify other limits. The grid is generated using No\_Of\_Spacings + 1 points along each direction. The known names for Units are angstroms, au and bohr.
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\subsection{SMEAR - Fractional Occupation of the Molecular Orbitals}
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\label{sec:band_smear}
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The smear keyword to turn on fractional occupation of the molecular orbitals
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\begin{verbatim}
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SMEAR <sigma default 0.001> [TEMPERATURE <temperature>] [FERMI || GAUSSIAN default FERMI]
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[ORBITALS <integer orbitals default 4>]
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\end{verbatim}
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Both Fermi-Dirac (FERMI) and Gaussian broadening functions are available. The ORBITALS keyword is used to change
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the number of virtual orbitals to be used in the calculation. Note to use this option the user must currently use the
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SCF minimizer. The following SCF option is recommended for running fractional occupation
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\begin{verbatim}
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SCF Anderson
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\end{verbatim}
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\section{PAW Tasks}
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@ -1485,6 +1620,7 @@ NWPW
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TIME_STEP <real time_step default 5.8>
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LOOP <integer inner_iteration outer_iteration default 10 100>
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TOLERANCES <real tole tolc default 1.0e-7 1.0e-7>
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CUTOFF <real cutoff>
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ENERGY_CUTOFF <real ecut default (see input description)>
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WAVEFUNCTION_CUTOFF <real wcut default (see input description)>
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EWALD_NCUT <integer ncut default 1>]
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@ -1526,6 +1662,9 @@ The following list describes these keywords.
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\item $<$outer\_iteration$>$ - number of outer iterations
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\item $<$tole$>$ - value for the energy tolerance.
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\item $<$tolc$>$ - value for the one-electron orbital tolerance.
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\item $<$cutoff$>$ - value for the cutoff energy used to define the wavefunction. In addition
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using the CUTOFF keyword automatically sets the cutoff energy for the density
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to be twice the wavefunction cutoff.
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\item $<$ecut$>$ - value for the cutoff energy used
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to define the density. Default is set
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to be the maximum value that will fit
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@ -2177,6 +2316,283 @@ task pspw optimize
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\end{verbatim}
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\normalsize
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\section{PSPW Tutorial 4: QM/MM simulation for CCl$_4$ + 64H$_2$O}
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\label{sec:pspw_qmmm_simulation}
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In this section we show how use the PSPW module to perform a Car-Parrinello
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QM/MM simulation for a CCl$_4$ molecule in a box of 64 H$_2$O.
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Before running a PSPW Car-Parrinello simulation the system should be
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on the Born-Oppenheimer surface, i.e. the one-electron orbitals should be minimized
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with respect to the total energy (i.e. task pspw energy).
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In the following example we show the input needed to run a Car-Parrinello
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QM/MM simulation for a CCl$_4$ molecule in a box of 64 H$_2$O.
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In this example, default pseudopotentials from the pseudopotential library are used
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for C, Cl, O\^\ and H\^\, exchange correlation functional is PBE96, The boundary condition is periodic, and
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with a side length of 23.577 Bohrs and has a cutoff energy is 50 Ry). The time step and fake mass
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for the Car-Parrinello run are specified to be 5.0 au and 600.0 au, respectively.
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\normalsize
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\begin{verbatim}
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title "CCl4 + water64 QM/MM simulation- 195 atom cell"
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memory 1500 mb
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start CCl4-water64
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#scratch_dir ./perm
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#permanent_dir ./perm
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\end{verbatim}
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\tiny
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\begin{verbatim}
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geometry nocenter noautoz noautosym
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C 0.7804E-02 -0.2897E-02 0.1420E-02 -0.2910E-07 -0.1055E-07 -0.2001E-07
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Cl -0.8603E+00 0.1547E+01 0.2556E+00 -0.2910E-07 -0.1055E-07 -0.2001E-07
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Cl 0.8421E+00 -0.4774E+00 0.1518E+01 -0.2910E-07 -0.1055E-07 -0.2001E-07
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Cl -0.1167E+01 -0.1279E+01 -0.4592E+00 -0.2910E-07 -0.1055E-07 -0.2001E-07
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Cl 0.1218E+01 0.1972E+00 -0.1309E+01 -0.2910E-07 -0.1055E-07 -0.2001E-07
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O^ 0.1545E+01 -0.3640E+01 -0.2558E+01 0.1675E-03 -0.2134E-03 0.2608E-03
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H^ 0.6377E+00 -0.4054E+01 -0.2486E+01 -0.8467E-05 -0.6710E-04 -0.1101E-02
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H^ 0.1860E+01 -0.3690E+01 -0.3506E+01 0.9734E-03 0.1042E-02 0.4566E-03
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O^ -0.6138E+01 -0.4627E+01 -0.1181E+01 -0.1477E-03 -0.1616E-03 -0.1670E-03
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H^ -0.7068E+01 -0.4458E+01 -0.8549E+00 -0.6948E-03 -0.5435E-03 -0.1521E-02
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H^ -0.5628E+01 -0.5133E+01 -0.4858E+00 -0.8855E-03 0.2768E-03 0.6961E-03
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O^ 0.3808E+01 0.2935E+01 0.2147E+01 -0.6374E-04 0.1081E-03 -0.3184E-04
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H^ 0.4187E+01 0.2253E+01 0.2772E+01 0.5832E-03 0.5155E-03 0.2134E-04
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H^ 0.4511E+01 0.3612E+01 0.1926E+01 -0.4943E-03 0.3230E-03 -0.7034E-03
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O^ -0.6210E+00 -0.5260E+01 -0.2842E+01 0.1727E-03 0.9623E-04 0.8184E-04
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H^ -0.2750E+00 -0.5523E+01 -0.3742E+01 0.1119E-03 0.7072E-03 -0.1203E-03
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H^ -0.7042E+00 -0.6073E+01 -0.2266E+01 -0.6331E-03 -0.4150E-03 -0.7442E-03
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O^ 0.2760E+01 0.2730E+01 -0.4774E+01 -0.1327E-03 0.3354E-03 -0.1366E-03
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H^ 0.3676E+01 0.2570E+01 -0.5142E+01 -0.5941E-04 0.5145E-03 -0.3057E-04
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H^ 0.2828E+01 0.2989E+01 -0.3811E+01 -0.2370E-03 0.1001E-02 -0.3029E-03
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O^ -0.2387E+01 0.5716E+01 0.3965E+01 -0.6296E-04 -0.1405E-04 -0.2853E-04
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H^ -0.1694E+01 0.5121E+01 0.3558E+01 0.5787E-04 -0.5014E-03 0.9024E-03
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H^ -0.1939E+01 0.6465E+01 0.4453E+01 -0.2046E-03 0.6948E-04 -0.2150E-04
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O^ -0.3456E+01 0.5123E+01 -0.2154E+01 -0.3714E-04 -0.1948E-03 0.4699E-05
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H^ -0.3043E+01 0.4342E+01 -0.2622E+01 -0.1119E-05 -0.3220E-03 0.2734E-03
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H^ -0.3693E+01 0.5826E+01 -0.2825E+01 -0.2085E-03 -0.4813E-03 -0.2351E-03
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O^ 0.5940E+00 0.1399E+01 0.3463E+01 -0.1288E-03 -0.9776E-04 -0.1409E-03
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H^ 0.1245E+01 0.1913E+01 0.2904E+01 -0.3790E-03 -0.4010E-03 -0.6948E-03
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H^ -0.3201E+00 0.1790E+01 0.3355E+01 -0.1070E-03 0.6148E-04 0.3431E-03
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O^ 0.4845E+01 0.4936E+01 0.4088E+01 0.2876E-03 -0.2625E-03 -0.7661E-04
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H^ 0.4098E+01 0.5168E+01 0.3465E+01 -0.1301E-03 -0.5756E-04 0.4909E-03
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H^ 0.4740E+01 0.3991E+01 0.4397E+01 0.1202E-02 -0.7660E-03 -0.1345E-02
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O^ -0.7209E+00 0.4285E+01 0.1237E+01 -0.1519E-03 0.6569E-04 0.1096E-03
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H^ 0.1958E-01 0.4499E+01 0.6000E+00 -0.5731E-04 -0.2919E-03 0.9929E-04
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H^ -0.1597E+01 0.4541E+01 0.8281E+00 -0.1117E-03 -0.3977E-03 -0.2666E-03
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O^ 0.3836E+01 0.2390E-01 -0.6670E+00 0.2697E-04 -0.6474E-05 -0.4852E-03
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H^ 0.4335E+01 -0.5028E+00 0.2166E-01 -0.1127E-02 0.1144E-02 0.1230E-02
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H^ 0.2962E+01 -0.4225E+00 -0.8598E+00 -0.1721E-03 0.3171E-03 -0.3321E-03
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O^ -0.7034E+00 -0.2120E+01 -0.3538E+01 0.1292E-03 -0.1072E-03 -0.1333E-03
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H^ -0.7567E+00 -0.3086E+01 -0.3284E+01 0.5037E-03 -0.2660E-03 -0.6455E-03
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H^ 0.2369E+00 -0.1894E+01 -0.3793E+01 0.2452E-03 0.6329E-03 0.9344E-03
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O^ 0.1465E+01 -0.4009E+01 0.4737E+01 0.3828E-03 -0.5067E-04 0.2649E-03
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H^ 0.4923E+00 -0.3944E+01 0.4958E+01 0.3572E-03 0.1205E-02 -0.2187E-03
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H^ 0.1582E+01 -0.4544E+01 0.3901E+01 0.1254E-03 -0.4486E-03 0.4761E-03
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O^ -0.3224E+01 -0.3091E+00 0.1701E+01 -0.2499E-03 -0.2643E-03 -0.1442E-03
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H^ -0.2950E+01 -0.9626E+00 0.9949E+00 -0.4237E-03 -0.8809E-04 -0.3749E-03
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H^ -0.3005E+01 0.6188E+00 0.1398E+01 -0.6682E-03 -0.1587E-03 -0.1246E-03
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O^ 0.5321E+01 0.3728E+01 -0.5992E+01 0.1243E-03 0.1407E-03 0.3011E-04
|
||||
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|
||||
O^ -0.5167E+01 0.9137E-01 0.4518E+01 -0.7764E-04 -0.2549E-04 0.4651E-03
|
||||
H^ -0.4490E+01 0.2494E+00 0.3799E+01 -0.5003E-03 -0.3149E-03 0.3790E-05
|
||||
H^ -0.5695E+01 0.9276E+00 0.4669E+01 -0.8687E-03 -0.3647E-03 -0.4836E-03
|
||||
end
|
||||
\end{verbatim}
|
||||
\normalsize
|
||||
\begin{verbatim}
|
||||
#set up the QM/MM simulation and cell
|
||||
NWPW
|
||||
SIMULATION_CELL
|
||||
SC 23.577
|
||||
END
|
||||
QMMM
|
||||
lj_ion_parameters C 3.41000000d0 0.10000000d0
|
||||
lj_ion_parameters Cl 3.45000000d0 0.16d0
|
||||
lj_ion_parameters O^ 3.16555789d0 0.15539425d0
|
||||
|
||||
# new input format
|
||||
fragment spc
|
||||
size 3
|
||||
index_start 6:195:3
|
||||
shake units angstroms 1 2 3 cyclic 1.0 1.632993125 1.0
|
||||
end
|
||||
END
|
||||
END
|
||||
|
||||
#***** Setup conjugate gradient code ****
|
||||
nwpw
|
||||
cutoff 25.0
|
||||
xc pbe96
|
||||
lmbfgs
|
||||
ewald_ncut 1
|
||||
end
|
||||
set nwpw:lcao_skip .true.
|
||||
task pspw energy
|
||||
|
||||
|
||||
#***** Setup Car-Parrinello code ****
|
||||
nwpw
|
||||
car-parrinello
|
||||
Nose-Hoover 1200.0 300.0 1200.0 300.0
|
||||
time_step 5.00
|
||||
fake_mass 750.0
|
||||
loop 10 2000
|
||||
xyz_filename ccl4.00.xyz
|
||||
ion_motion_filename ccl4.00.ion_motion
|
||||
emotion_filename ccl4.00.emotion
|
||||
end
|
||||
end
|
||||
task pspw car-parrinello
|
||||
|
||||
\end{verbatim}
|
||||
|
||||
|
||||
|
||||
|
||||
|
|
@ -2276,21 +2692,71 @@ nwpw
|
|||
end
|
||||
ewald_ncut 8
|
||||
monkhorst-pack 2 2 2
|
||||
lmbfgs
|
||||
end
|
||||
set nwpw:minimizer 2
|
||||
|
||||
driver
|
||||
clear
|
||||
maxiter 40
|
||||
end
|
||||
set includestress .true. # this option tells driver to optimize the unit cell
|
||||
set nwpw:stress_numerical .true. #currently only numerical stresses are working with band
|
||||
#set nwpw:stress_numerical .true. #option to use numerical stresses
|
||||
|
||||
task band optimize
|
||||
|
||||
\end{verbatim}
|
||||
|
||||
|
||||
\normalsize
|
||||
\section{BAND Tutorial 3: optimizing a unit cell and geometry for Aluminum with fractional occupation}
|
||||
\label{sec:band_unitcell_optimization}
|
||||
|
||||
The following example demonstrates how to uses the BAND module to optimize the unit cell
|
||||
and geometry for a Aluminum.
|
||||
|
||||
\begin{verbatim}
|
||||
title "Aluminum optimization with fractional occupation"
|
||||
|
||||
start aluminumfrac
|
||||
|
||||
memory 900 mb
|
||||
|
||||
geometry noautoz
|
||||
system crystal
|
||||
lat_a 3.0
|
||||
lat_b 3.0
|
||||
lat_c 3.0
|
||||
alpha 90.0
|
||||
beta 90.0
|
||||
gamma 90.0
|
||||
end
|
||||
Al 0.0 0.0 0.0
|
||||
Al 0.0 0.5 0.5
|
||||
Al 0.5 0.5 0.0
|
||||
Al 0.5 0.0 0.5
|
||||
end
|
||||
set nwpw:cif_filename aluminum
|
||||
|
||||
nwpw
|
||||
scf anderson
|
||||
mult 1
|
||||
smear temperature 3500.0 fermi
|
||||
cutoff 15.0
|
||||
monkhorst-pack 3 3 3
|
||||
ewald_ncut 8
|
||||
mapping 2
|
||||
end
|
||||
set nwpw:lcao_skip .true.
|
||||
|
||||
set includestress .true.
|
||||
#set nwpw:stress_numerical .true.
|
||||
|
||||
driver
|
||||
clear
|
||||
end
|
||||
task band optimize ignore
|
||||
|
||||
\end{verbatim}
|
||||
|
||||
|
||||
|
||||
|
|
|
|||
Loading…
Add table
Add a link
Reference in a new issue