CASINO manual - Theory of Condensed Matter

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4 Input geometry C 0.000000 0.000000 0.000000 5.000000 H -1.407651 -1.138185 0.054434 -1.000000 H 0.894354 0.554315 1.263301 -1.000000 H 0.528074 1.081535 -0.755823 -1.000000 4 Input geometry C 0.000000 0.000000 0.000000 5.000000 H -1.407651 -1.138185 0.054434 -1.000000 H 0.894354 0.554315 1.263301 -1.000000 H 0.528074 1.081535 -0.755823 -1.000000 (etc.) Notes: 1. The movie.out file follows the standard (x, y, z) molecular format. 2. Line 1 indicates the total number n of ions and particles. 3. Line 2 is a comment. 4. The following n lines consist of five columns. Column 1 specifies the type of particle (H=electron, O=hole and C=other atoms). Columns 2, 3 and 4 are the x, y and z coordinates of the particle. Column 5 specifies the charge of the particle. 5. This information is then repeated. The total number of sets of geometry contained in movie.out is controlled by the keywords vmc equil nstep, vmc nstep and movieplot in the input file. 6. For column 1, the ‘H=electron, O=hole and C=other atoms’ convention is somewhat confusing, but is necessary because particles have to take on element symbols in order for the standard visualization programs to read the movie.out file. 7. Column 5 is not read by the visualization programs. It is only there so that different types of particle can be distinguished. 11.2 Visualization Having generated the movie.out file we are able to visualize the results using vmd or jmol. (This information probably needs updating!) 11.2.1 VMD vmd (Visual Molecular Dynamics) is a molecular visualization program. It supports computers running MacOS-X, Unix, or Windows, is distributed free of charge, and includes source code. VMC can be downloaded from www.ks.uiuc.edu/Research/vmd/. • Type vmd. A ‘VMD console’ and a ‘VMD Display’ window will appear. • In the ‘VMD console’ window type menu main on. An extra ‘VMD Main’ menu bar will appear. • On the ‘VMD Main’ menu bar, click on File → New Molecule. A ‘Molecule File Browser’ will appear. • In the ‘Molecule File Browser’, browse for the file movie.out and choose the file type to be xyz. Click Load to open the file. • On ‘VMD Main’, click on Graphics → Representations. A ‘Graphical Representations’ menu bar will pop up. Choose CPK as the drawing method, the bond resolution to be 1 and the sphere resolution to be 15. Click Apply. • On ‘VMD Main’, click on Extensions → vmdmovie. (For version 1.8.3, click on Extensions → Visualization → Movie Maker.) A ‘VMD Movie Generator’ will pop up. 120
• In Movie Settings choose Trajectory. The movie can be saved in the AVI or MPEG format. Choose by clicking on Format and tick the preferred format. Then check whether the name of the temporary directory suggested is right (this is where the RGB files are created). Note that this directory should be free of RGB files belonging to other users. If this has to be changed then click on the Set working directory button and browse for the directory. • Type in the name of the movie in the box provided. Click on the Make Movie button. • The movie will be displayed in the Open GL Display screen. The .mpg or .avi movie file will be produced in the working directory being specified. They have to be viewed with other viewers, for example mpeg play for .mpg files. For an example movie made with vmd (a casino VMC simulation of cyclohexane) see www.tcm.phy. cam.ac.uk/~mdt26/downloads/cyclohexane2.mpg. 11.2.2 JMOL jmol is a free, open source molecule viewer. It supports computers running Windows, Mac OS X and Linux/Unix systems. Jmol can be downloaded from jmol.sourceforge.net/ • Type jmol. Click on File→ Open. Browse for the file movie.out and click Open. • Click on Display and untick the box for Bonds. • Click on Extras → Animate. An animation tool bar will appear. To start the movie click on the ‘play’ symbol. 12 Detailed information: the VMC method 12.1 Evaluating expectation values The expectation value of the Hamiltonian Ĥ with respect to the trial wave function Ψ can be written as ∫ 〈Ĥ〉 = EL (R)|Ψ(R)| 2 dR ∫ |Ψ(R)|2 dR , (11) −1 where E L (R) = Ψ (R)Ĥ(R)Ψ(R) is the local energy. We can evaluate this expectation value by using the Metropolis algorithm [24] to generate a sequence of configurations R distributed according to |Ψ(R)| 2 and averaging the corresponding local energies. 12.2 The sampling algorithm The implementation of VMC in casino involves making trial moves, whether of a single electron or of the entire configuration, and accepting or rejecting the moves in accordance with the Metropolis algorithm. The Metropolis transition probability density is Gaussian of variance τ, where τ is the VMC time step (dtvmc). In the electron-by-electron algorithm, each step consists in proposing individual moves for each of the electrons and subject each move to a separate accept/reject step. In the configuration-by-configuration algorithm one configuration move is proposed per step, and is accepted or rejected as a whole. Another difference in the casino implementation of these two methods is that in the configuration-byconfiguration the local energy (and all other expectation values) are evaluated both before and after the move, and it is the average of the two, weighted by the acceptance probability, that enters the accumulation arrays. In the electron-by-electron algorithm we only evaluate the energy after having moved the configuration. The configuration-by-configuration algorithm has the disadvantage of suffering from long correlation times, which makes it in practice more expensive than the electron-by-electron algorithm in virtually all cases. Thus we will restrict our discussion below to the electron-by-electron algorithm. 121
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CASINO User’s Guide Version 2.13
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8.6 GAUSSIAN94/98/03/09 . . . . . .
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29.2 Fourier transformation of CASI
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1 Introduction casino is a computer
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3.2 Legal stuff casino is given awa
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- Grossman-Mitas DMC-DFT molecular
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Your defined setup can then be perm
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- : perform compilation (default).
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6 Introductory user’s guide: how
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ATOM BASIS TYPE The basis used to r
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ENVMC v0.60: Script to extract VMC
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Std. err. in the mean DMC energy (a
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Jastrow factor from each cycle of t
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V(x) Ψ init (x) τ{ t Ψ 0 (x) x T
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the energy becomes roughly constant
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many cores, time limits etc, which
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Set the verbosity level of the mach
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6.7 How to run coupled DFT-DMC mole
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unqmcmd --startqmc=M Start the chai
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config.out This is the name under w
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‘slater-type’: use Slater-type
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CUSTOM SPAIR DEP (Block) This input
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initial configurations come from DM
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DTDMC (Real) Time step for DMC run
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FORCES INFO (Integer) Controls the
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nucleus is assumed to lie at the or
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MOVIECELLS (Logical) If F then casi
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OPT MAXITER (Integer) Largest permi
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of G vectors and discards all those
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half a million cores, it may be des
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VM REWEIGHT (Logical) If vm reweigh
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default this is 0 hartree. It shoul
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A very detailed specification of th
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-1 0 0 1 1 1 1 1 1 1 0 2 1 0 1 2 Pa
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cusp conditions; otherwise, only th
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Detailed information about each of
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|k| (outermost). Hence one can spec
Page 75 and 76: large and the wave function is near
Page 77 and 78: R(i) in atomic units 0.000000000000
Page 79 and 80: 2. The charge-density Fourier coeff
Page 81 and 82: c_767: [ 996 ] ... Compressed expan
Page 83 and 84: valence charges for each atom %%%%%
Page 85 and 86: 1988). This can be found online. An
Page 87 and 88: 1.3813695578425E+00 1.3957621401173
Page 89 and 90: PWSCF Method: DFT DFT Functional: u
Page 91 and 92: 0.125203784849961E-01 0.13042462855
Page 93 and 94: 3.3000000000000E+00 2.0000000000000
Page 95 and 96: Potential Number of grid points 200
Page 97 and 98: 9. Clearly, the total number of pos
Page 99 and 100: EBEST (DMC only) Best estimate of t
Page 101 and 102: Use G-vector set 1 Number of sets 2
Page 103 and 104: 1000.0 rho_a(G)*rho_b(-G) 16.0 4.12
Page 105 and 106: total weight must always be include
Page 107 and 108: The exporter does not currently wor
Page 109 and 110: 8.4.2 Generating gwfn.data files wi
Page 111 and 112: After successfully running properti
Page 113 and 114: % mv Test.FChk dna.Fchk run gaussia
Page 115 and 116: • By default, gaussian uses spin
Page 117 and 118: Routine Purpose qmc write Writes th
Page 119 and 120: not the case the defaults can be ch
Page 121 and 122: 8.10 TURBOMOLE Website: www.turbomo
Page 123 and 124: • crysgen06/09, crystaltoqmc: The
Page 125: • quickblock: Simple reblocking u
Page 129 and 130: the move rejection probability is h
Page 131 and 132: This leads to the single-electron d
Page 133 and 134: In the UNR [19] scheme the modified
Page 135 and 136: 13.7 Evaluating expectation values
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Page 139 and 140: where u k has the periodicity of th
Page 141 and 142: Although the constraint equations a
Page 143 and 144: 18 Wave-function updating Consider
Page 145 and 146: 19.2 Evaluating the nonlocal pseudo
Page 147 and 148: of a unit point charge at r j in ev
Page 149 and 150: 19.4.3 1D Coulomb interaction Coulo
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Page 153 and 154: correlations, such as might be enco
Page 155 and 156: where n is the order of the expansi
Page 157 and 158: terms by definition, and it can be
Page 159 and 160: which is therefore independent of r
Page 161 and 162: where the local energy, E L , is E
Page 163 and 164: Another variant of variance minimiz
Page 165 and 166: The energy minimization method used
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Page 173 and 174: that the number of configuration mo
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0.5 0.5 0.0 particle 1 det 1 : 9 or
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The clearup twistav script can be u
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In the infinite system limit, the s
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Note that this has the k −2 diver
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• The effective time step, Eq. (3
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1 2 H He 1.00794 4.00260 3 4 5 6 7
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and the Dirac delta function is δ(
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33.2.2 Atomic densities K eywords:
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The spin-density matrix is a two-by
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33.3.3 Homogeneous and isotropic sy
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33.4 Structure factor and spherical
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33.5 One-body density matrix, two-b
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[ where the approximation ρ (1)T
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The figure shows the localization l
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with F HFT mix = − F P mix = −
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The input keyword to activate the c
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To each walker r j , we assign a li
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37 Magnetic fields and the fixed-ph
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38 Analysis of the performance of C
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the orbitals, α = 2 [11]. The use
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39.2 Implementation basics and perf
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• Use ‘endif’ and ‘enddo’
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• Evidence of testing on serial a
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B Appendix 2: Automatic testing of
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• Delete any eepot.data and densi
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* "Generic" CASINO_ARCHs are intend
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- ‘head -n 1 /etc/redhat-release
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for a single job in an ensemble of
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inary executable. CASINO does not r
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otherwise. The following tags are o
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[2] V.R. Saunders, R. Dovesi, C. Ro
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[50] W. Janke, Statistical Analysis
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CASINO manual - Theory of Condensed Matter

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