From 8445af45fe881170846d45e96dc8b800bd04469e Mon Sep 17 00:00:00 2001 From: Eric Bylaska Date: Fri, 21 Dec 2007 18:48:11 +0000 Subject: [PATCH] 5.1 updates...EJB --- doc/user/pspw.tex | 476 +++++++++++++++++++++++++++++++++++++++++++++- 1 file changed, 471 insertions(+), 5 deletions(-) diff --git a/doc/user/pspw.tex b/doc/user/pspw.tex index eb123d7320..048af20cce 100644 --- a/doc/user/pspw.tex +++ b/doc/user/pspw.tex @@ -1,5 +1,5 @@ % -% $Id: pspw.tex,v 1.42 2006-09-28 19:48:08 bylaska Exp $ +% $Id: pspw.tex,v 1.43 2007-12-21 18:48:11 bylaska Exp $ % \label{sec:pspw} @@ -118,6 +118,7 @@ PSPW TIME_STEP LOOP TOLERANCES + CUTOFF ENERGY_CUTOFF WAVEFUNCTION_CUTOFF EWALD_NCUT ] @@ -170,7 +171,10 @@ The following list describes the keywords contained in the PSPW input block. \item $<$outer\_iteration$>$ - number of outer iterations \item $<$tole$>$ - value for the energy tolerance. \item $<$tolc$>$ - value for the one-electron orbital tolerance. - \item $<$edit$>$ - value for the cutoff energy used + \item $<$cutoff$>$ - value for the cutoff energy used to define the wavefunction. In addition + using the CUTOFF keyword automatically sets the cutoff energy for the density + to be twice the wavefunction cutoff. + \item $<$ecut$>$ - value for the cutoff energy used to define the density. Default is set to be the maximum value that will fit within the simulation\_cell $<$cell\_name$>$. @@ -765,6 +769,117 @@ center of mass shifting. This can be done by the following \verb+SET+ directive. set nwpw:com_shift .false. \end{verbatim} +\subsection{\tt QM/MM} +\label{sec:pspw_qmmm} +A preliminary QM/MM capability that can run Car-Parrinello molecular dynamics has been integrated +into the PSPW module. Currently, the input is not very robust but it is straightforward. The first +step to run a QM/MM simulations is to define the MM atoms in the geometry block. The MM atoms must be +at the end of the geometry and a carat, " \^\ ", must be appended to the end of the atom name, e.g. +\begin{verbatim} +geometry units angstrom nocenter noautosym noautoz print xyz +C -0.000283 0.000106 0.000047 +Cl -0.868403 1.549888 0.254229 +Cl 0.834043 -0.474413 1.517103 +Cl -1.175480 -1.275747 -0.460606 +Cl 1.209940 0.200235 -1.310743 + +O^ 0.3226E+01 -0.4419E+01 -0.5952E+01 +H^ 0.3193E+01 -0.4836E+01 -0.5043E+01 +H^ 0.4167E+01 -0.4428E+01 -0.6289E+01 +O^ 0.5318E+01 -0.3334E+01 -0.1220E+01 +H^ 0.4978E+01 -0.3040E+01 -0.2113E+01 +H^ 0.5654E+01 -0.2540E+01 -0.7127E+00 +end +\end{verbatim} +Next the pseudopotentials have be defined for the every type of MM atom contained in the geometry blocks. The +following local pseudopotential suggested by Laio, VandeVondele and Rothlisberger can be automatically generated. +\begin{eqnarray} +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}} +\end{eqnarray} +The following input To define this pseudopo the O\^\ MM atom using the following input +\begin{verbatim} +NWPW + QMMM + mm_psp O^ -0.8476 4 0.70 + END +END +\end{verbatim} +defines the local pseudopotential for the O\^\ MM atom , where $Z_{ion}=-0.8476$, $n_{\sigma}=4$, and $r_c=0.7$. +The following input can be used to define the local pseudopotentials for all the MM atoms in the geometry +block defined above +\begin{verbatim} +NWPW + QMMM + mm_psp O^ -0.8476 4 0.70 + mm_psp H^ 0.4238 4 0.40 + END +END +\end{verbatim} +Next the Lenard-Jones potentials for the QM and MM atoms need to be defined. This is done as as follows +\begin{verbatim} +NWPW + QMMM + lj_ion_parameters C 3.41000000d0 0.10d0 + lj_ion_parameters Cl 3.45000000d0 0.16d0 + lj_ion_parameters O^ 3.16555789d0 0.15539425d0 + END +END +\end{verbatim} +Note that the Lenard-Jones potential is not defined for the MM H atoms in this example. +The final step is to define the MM fragments in the simulation. MM fragments are a set of +atoms in which bonds and angle harmonic potentials are defined, or alternatively shake constraints are defined. +The following input defines the fragments for the two water molecules in the above geometry, +\begin{verbatim} +NWPW + QMMM + fragment spc + size 3 #size of fragment + index_start 6:9:3 #atom index list that defines the start of + # the fragments (start:final:stride) + + bond_spring 1 2 0.467307856 1.889726878 #bond i j Kspring r0 + bond_spring 1 3 0.467307856 1.889726878 #bond i j Kspring r0 + angle_spring 2 1 3 0.07293966 1.910611932 #angle i j k Kspring theta0 + end + END +END +\end{verbatim} +The fragments can be defined using shake constraints as +\begin{verbatim} +NWPW + QMMM + fragment spc + size 3 #size of fragment + index_start 6:9:3 #atom index list that defines the start of + # the fragments (start:final:stride) + + shake units angstroms 1 2 3 cyclic 1.0 1.632993125 1.0 + end + END +END +\end{verbatim} +Alternatively, each water could be defined independently as follows. +\begin{verbatim} +NWPW + QMMM + fragment spc1 + size 3 #size of fragment + index_start 6 #atom index list that defines the start of + #the fragments + + bond_spring 1 2 0.467307856 1.889726878 #bond i j Kspring r0 + bond_spring 1 3 0.467307856 1.889726878 #bond i j Kspring r0 + angle_spring 2 1 3 0.07293966 1.910611932 #angle i j k Kspring theta0 + end + fragment spc2 + size 3 #size of fragment + index_start 9 #atom index list that defines the start of + #the fragments + shake units angstroms 1 2 3 cyclic 1.0 1.632993125 1.0 + end + END +END +\end{verbatim} \subsection{\tt PSP\_GENERATOR} @@ -1268,6 +1383,7 @@ NWPW TIME_STEP LOOP TOLERANCES + CUTOFF ENERGY_CUTOFF WAVEFUNCTION_CUTOFF EWALD_NCUT ] @@ -1283,6 +1399,8 @@ NWPW BAND_DPLOT ... (see input description) END MAPPING + SMEAR [TEMPERATURE ] [FERMI || GAUSSIAN default FERMI] + [ORBITALS ] END \end{verbatim} @@ -1305,6 +1423,9 @@ The following list describes these keywords. \item $<$outer\_iteration$>$ - number of outer iterations \item $<$tole$>$ - value for the energy tolerance. \item $<$tolc$>$ - value for the one-electron orbital tolerance. + \item $<$cutoff$>$ - value for the cutoff energy used to define the wavefunction. In addition + using the CUTOFF keyword automatically sets the cutoff energy for the density + to be twice the wavefunction cutoff. \item $<$ecut$>$ - value for the cutoff energy used to define the density. Default is set to be the maximum value that will fit @@ -1329,6 +1450,8 @@ The following list describes these keywords. \item BRILLOUIN\_ZONE (see section \ref{sec:band_brillouin_zone}) \item MONKHORST-PACK - Alternatively, the MONKHORST-PACK keyword can be used to enter a MONKHORST-PACK sampling of the Brillouin zone. + \item $<$smear$>$ - value for smearing broadending + \item $<$temperature$>$ - same as smear but in units of K. \end{itemize} @@ -1438,7 +1561,19 @@ This sub-directive specifies the molecular orbital number that is to be plotted. \end{verbatim} 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. - +\subsection{SMEAR - Fractional Occupation of the Molecular Orbitals} +\label{sec:band_smear} +The smear keyword to turn on fractional occupation of the molecular orbitals +\begin{verbatim} + SMEAR [TEMPERATURE ] [FERMI || GAUSSIAN default FERMI] + [ORBITALS ] +\end{verbatim} +Both Fermi-Dirac (FERMI) and Gaussian broadening functions are available. The ORBITALS keyword is used to change +the number of virtual orbitals to be used in the calculation. Note to use this option the user must currently use the +SCF minimizer. The following SCF option is recommended for running fractional occupation +\begin{verbatim} + SCF Anderson +\end{verbatim} \section{PAW Tasks} @@ -1485,6 +1620,7 @@ NWPW TIME_STEP LOOP TOLERANCES + CUTOFF ENERGY_CUTOFF WAVEFUNCTION_CUTOFF EWALD_NCUT ] @@ -1526,6 +1662,9 @@ The following list describes these keywords. \item $<$outer\_iteration$>$ - number of outer iterations \item $<$tole$>$ - value for the energy tolerance. \item $<$tolc$>$ - value for the one-electron orbital tolerance. + \item $<$cutoff$>$ - value for the cutoff energy used to define the wavefunction. In addition + using the CUTOFF keyword automatically sets the cutoff energy for the density + to be twice the wavefunction cutoff. \item $<$ecut$>$ - value for the cutoff energy used to define the density. Default is set to be the maximum value that will fit @@ -2177,6 +2316,283 @@ task pspw optimize \end{verbatim} +\normalsize +\section{PSPW Tutorial 4: QM/MM simulation for CCl$_4$ + 64H$_2$O} +\label{sec:pspw_qmmm_simulation} + +In this section we show how use the PSPW module to perform a Car-Parrinello +QM/MM simulation for a CCl$_4$ molecule in a box of 64 H$_2$O. +Before running a PSPW Car-Parrinello simulation the system should be +on the Born-Oppenheimer surface, i.e. the one-electron orbitals should be minimized +with respect to the total energy (i.e. task pspw energy). + +In the following example we show the input needed to run a Car-Parrinello +QM/MM simulation for a CCl$_4$ molecule in a box of 64 H$_2$O. +In this example, default pseudopotentials from the pseudopotential library are used +for C, Cl, O\^\ and H\^\, exchange correlation functional is PBE96, The boundary condition is periodic, and +with a side length of 23.577 Bohrs and has a cutoff energy is 50 Ry). The time step and fake mass +for the Car-Parrinello run are specified to be 5.0 au and 600.0 au, respectively. +\normalsize +\begin{verbatim} +title "CCl4 + water64 QM/MM simulation- 195 atom cell" + +memory 1500 mb +start CCl4-water64 + +#scratch_dir ./perm +#permanent_dir ./perm +\end{verbatim} +\tiny +\begin{verbatim} +geometry nocenter noautoz noautosym +C 0.7804E-02 -0.2897E-02 0.1420E-02 -0.2910E-07 -0.1055E-07 -0.2001E-07 +Cl -0.8603E+00 0.1547E+01 0.2556E+00 -0.2910E-07 -0.1055E-07 -0.2001E-07 +Cl 0.8421E+00 -0.4774E+00 0.1518E+01 -0.2910E-07 -0.1055E-07 -0.2001E-07 +Cl -0.1167E+01 -0.1279E+01 -0.4592E+00 -0.2910E-07 -0.1055E-07 -0.2001E-07 +Cl 0.1218E+01 0.1972E+00 -0.1309E+01 -0.2910E-07 -0.1055E-07 -0.2001E-07 + +O^ 0.1545E+01 -0.3640E+01 -0.2558E+01 0.1675E-03 -0.2134E-03 0.2608E-03 +H^ 0.6377E+00 -0.4054E+01 -0.2486E+01 -0.8467E-05 -0.6710E-04 -0.1101E-02 +H^ 0.1860E+01 -0.3690E+01 -0.3506E+01 0.9734E-03 0.1042E-02 0.4566E-03 +O^ -0.6138E+01 -0.4627E+01 -0.1181E+01 -0.1477E-03 -0.1616E-03 -0.1670E-03 +H^ -0.7068E+01 -0.4458E+01 -0.8549E+00 -0.6948E-03 -0.5435E-03 -0.1521E-02 +H^ -0.5628E+01 -0.5133E+01 -0.4858E+00 -0.8855E-03 0.2768E-03 0.6961E-03 +O^ 0.3808E+01 0.2935E+01 0.2147E+01 -0.6374E-04 0.1081E-03 -0.3184E-04 +H^ 0.4187E+01 0.2253E+01 0.2772E+01 0.5832E-03 0.5155E-03 0.2134E-04 +H^ 0.4511E+01 0.3612E+01 0.1926E+01 -0.4943E-03 0.3230E-03 -0.7034E-03 +O^ -0.6210E+00 -0.5260E+01 -0.2842E+01 0.1727E-03 0.9623E-04 0.8184E-04 +H^ -0.2750E+00 -0.5523E+01 -0.3742E+01 0.1119E-03 0.7072E-03 -0.1203E-03 +H^ -0.7042E+00 -0.6073E+01 -0.2266E+01 -0.6331E-03 -0.4150E-03 -0.7442E-03 +O^ 0.2760E+01 0.2730E+01 -0.4774E+01 -0.1327E-03 0.3354E-03 -0.1366E-03 +H^ 0.3676E+01 0.2570E+01 -0.5142E+01 -0.5941E-04 0.5145E-03 -0.3057E-04 +H^ 0.2828E+01 0.2989E+01 -0.3811E+01 -0.2370E-03 0.1001E-02 -0.3029E-03 +O^ -0.2387E+01 0.5716E+01 0.3965E+01 -0.6296E-04 -0.1405E-04 -0.2853E-04 +H^ -0.1694E+01 0.5121E+01 0.3558E+01 0.5787E-04 -0.5014E-03 0.9024E-03 +H^ -0.1939E+01 0.6465E+01 0.4453E+01 -0.2046E-03 0.6948E-04 -0.2150E-04 +O^ -0.3456E+01 0.5123E+01 -0.2154E+01 -0.3714E-04 -0.1948E-03 0.4699E-05 +H^ -0.3043E+01 0.4342E+01 -0.2622E+01 -0.1119E-05 -0.3220E-03 0.2734E-03 +H^ -0.3693E+01 0.5826E+01 -0.2825E+01 -0.2085E-03 -0.4813E-03 -0.2351E-03 +O^ 0.5940E+00 0.1399E+01 0.3463E+01 -0.1288E-03 -0.9776E-04 -0.1409E-03 +H^ 0.1245E+01 0.1913E+01 0.2904E+01 -0.3790E-03 -0.4010E-03 -0.6948E-03 +H^ -0.3201E+00 0.1790E+01 0.3355E+01 -0.1070E-03 0.6148E-04 0.3431E-03 +O^ 0.4845E+01 0.4936E+01 0.4088E+01 0.2876E-03 -0.2625E-03 -0.7661E-04 +H^ 0.4098E+01 0.5168E+01 0.3465E+01 -0.1301E-03 -0.5756E-04 0.4909E-03 +H^ 0.4740E+01 0.3991E+01 0.4397E+01 0.1202E-02 -0.7660E-03 -0.1345E-02 +O^ -0.7209E+00 0.4285E+01 0.1237E+01 -0.1519E-03 0.6569E-04 0.1096E-03 +H^ 0.1958E-01 0.4499E+01 0.6000E+00 -0.5731E-04 -0.2919E-03 0.9929E-04 +H^ -0.1597E+01 0.4541E+01 0.8281E+00 -0.1117E-03 -0.3977E-03 -0.2666E-03 +O^ 0.3836E+01 0.2390E-01 -0.6670E+00 0.2697E-04 -0.6474E-05 -0.4852E-03 +H^ 0.4335E+01 -0.5028E+00 0.2166E-01 -0.1127E-02 0.1144E-02 0.1230E-02 +H^ 0.2962E+01 -0.4225E+00 -0.8598E+00 -0.1721E-03 0.3171E-03 -0.3321E-03 +O^ -0.7034E+00 -0.2120E+01 -0.3538E+01 0.1292E-03 -0.1072E-03 -0.1333E-03 +H^ -0.7567E+00 -0.3086E+01 -0.3284E+01 0.5037E-03 -0.2660E-03 -0.6455E-03 +H^ 0.2369E+00 -0.1894E+01 -0.3793E+01 0.2452E-03 0.6329E-03 0.9344E-03 +O^ 0.1465E+01 -0.4009E+01 0.4737E+01 0.3828E-03 -0.5067E-04 0.2649E-03 +H^ 0.4923E+00 -0.3944E+01 0.4958E+01 0.3572E-03 0.1205E-02 -0.2187E-03 +H^ 0.1582E+01 -0.4544E+01 0.3901E+01 0.1254E-03 -0.4486E-03 0.4761E-03 +O^ -0.3224E+01 -0.3091E+00 0.1701E+01 -0.2499E-03 -0.2643E-03 -0.1442E-03 +H^ -0.2950E+01 -0.9626E+00 0.9949E+00 -0.4237E-03 -0.8809E-04 -0.3749E-03 +H^ -0.3005E+01 0.6188E+00 0.1398E+01 -0.6682E-03 -0.1587E-03 -0.1246E-03 +O^ 0.5321E+01 0.3728E+01 -0.5992E+01 0.1243E-03 0.1407E-03 0.3011E-04 +H^ 0.5383E+01 0.3541E+01 -0.5012E+01 0.2175E-03 -0.4499E-04 0.4888E-05 +H^ 0.5850E+01 0.3045E+01 -0.6496E+01 -0.1043E-03 0.1021E-03 -0.1441E-03 +O^ -0.3365E+01 -0.2780E+01 0.3200E+01 0.2012E-03 -0.1310E-03 -0.1047E-04 +H^ -0.4036E+01 -0.2193E+01 0.3653E+01 -0.5141E-03 -0.4867E-03 -0.6379E-03 +H^ -0.3029E+01 -0.2327E+01 0.2375E+01 0.8564E-03 0.1057E-03 0.3940E-03 +O^ -0.6115E+01 0.4096E+01 -0.1385E+01 -0.2067E-03 -0.2544E-03 0.9568E-04 +H^ -0.6740E+01 0.3315E+01 -0.1402E+01 -0.7231E-04 -0.3492E-03 -0.2122E-03 +H^ -0.5445E+01 0.4002E+01 -0.2121E+01 -0.1573E-03 0.1356E-03 0.9095E-04 +O^ -0.1742E+01 0.5855E+01 -0.5125E+01 -0.4122E-03 -0.4759E-04 -0.3874E-04 +H^ -0.1849E+01 0.6848E+01 -0.5063E+01 0.6007E-03 0.8115E-04 -0.2854E-03 +H^ -0.9641E+00 0.5640E+01 -0.5716E+01 -0.3814E-03 -0.9778E-03 0.3468E-03 +O^ 0.3739E+01 0.4907E+01 -0.2428E+00 -0.1192E-05 -0.2368E-03 0.6724E-04 +H^ 0.3792E+01 0.3995E+01 0.1643E+00 -0.1132E-02 -0.3235E-03 0.1695E-04 +H^ 0.4347E+01 0.4954E+01 -0.1035E+01 -0.9395E-03 -0.1354E-02 -0.7298E-03 +O^ 0.2987E+00 -0.5628E+01 -0.8431E-01 -0.1166E-03 0.1187E-03 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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}