Mobile Chemistry Portal
hosted by J. Heyrovskı
Institute of Physical Chemistry of the CAS, v.v.i.
(Department of Molecular Electrochemistry and Catalysis)
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Mobile Chemistry Portal hosted by J. Heyrovskı
Institute of Physical Chemistry of the CAS, v.v.i.
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Siam Quantum Authors
Teepanis Chachiyo, Hathaithip Chachiyo (authors)
Homepage
The project
homepage
contains the complete info. The project is located at
GitHub
as well. Source code is available in the project homepage and at GitHub. Reference
Chachiyo, T. et al.: Siam Quantum: a compact open-source quantum
simulation software for molecules, Thailand (2016); Description & Use Siam Quantum offers wide computational methodology possibilities from ab initio through DFT, perturbation theory up to molecular dynamics. Both single point and geometry optimization procedures are available. Quick start Siam Quantum accepts as the input file directly the .xyz coordinate file produced by e.g. Atomdroid. The basis in the GAMESS-US style is saved as a text file. The keywords controlling the calculation are listed below, and are not a part of the input .xyz file, but they are filled in the execution command. Use in command line / shell:
sq [input file].xyz [basis file].txt [options] > [output file]
or
./sq [input file].xyz [basis file].txt [options] > [output file] The result will appear in the same location. Available switches: [x] Ab Initio Method: -HF Hartree-Fock (default) Density Functional Theory -LDA=S:VWN5 ex: Slater corr: VWN5 -LDA=S:CHACHIYO ex: Slater corr: Chachiyo -DFT=HALF ex: 0.5*(HF+Slater) corr: VWN5 -DFT=PBE ex: PBE corr: PBE -DFT=BLYP ex: Becke88 corr: LYP -DFT=CHACHIYO ex: Chachiyo corr: Chachiyo -DFT=B3LYP The famous Becke's three parameters hybrid -LIBXC=STR Use LibXC with specific ex. and corr. See its website for the avialable functionals Example, -LIBXC=GGA_X_CHACHIYO+GGA_C_CHACHIYO -LIBXC=HYB_GGA_XC_B3LYP -Q=INT Set total molecular charge (default=0) -M=INT Set molecular spin multiplicity (M=2S+1) -R Use restricted orbitals (default if singlet) -U Use unrestricted orbitals (default if M > 1 )
[x] Compute DFT exchange from Hartree-Fock densities: -xSlater Slater LDA exchange -xPerdewYue J.P.Perdew and W.Yue 1986 exchange -xPBE Perdew¾Burke¾Ernzerhof exchange -xBecke88 A.D.Becke 1988 exchange -xMVS meta-GGA Made Very Simple exchange -xChachiyo T.Chachiyo and H.Chachiyo exchange
[x] Post SCF: -FORCE Compute forces acting on nuclei -OPT Request geometry optimization -MP2 Request MP2 energy calculations -MECP=INT,INT Request MECP between two spin multiplicities -EXCITE Request excited state calculations -QMD Request quantum molecular dynamics simulation [x] SCF Cycle: -GUESS=DIAG Use identity density matrix as initial guess (default) -GUESS=CORE Use density from core hamiltonian as initial guess -GUESS=CHECK Use density from checkpoint as initial guess -SCFDIIS Use 4-point DIIS method for convergence (default) -SCFDIIS3 Use 3-point DIIS method for convergence -SCFDIIS2 Use 2-point DIIS method for convergence -SCFDAMP Use simple weighting method for convergence -SCFDRAG=REAL Set SCF drag coefficient between 0 to 1 (default=0.25) -SCFCONV=REAL Set SCF convergence threshold (default=1.0E-6) -SCFMAX=INT Set maximum number of scf cycle (default=80) -SCFACC=3STEP Use increasing integral accuracy in 3 steps (default) -SCFACC=1STEP Use fixed integral accuracy -MAXMEM=INT Set maximum memory per CPU in Mbyte (default=250)
[x] Grid: -GRIDSIZE=S Good enough for a few milli-hartree accuracy -GRIDSIZE=M Below milli-hartree (default for energy run) -GRIDSIZE=L A few micro hartree (default for optimization) -GRIDSIZE=XL Good for testing (96/590 radial/anuglar point) -GRID=BALLS Use Becke partition + uniform radius (default) -GRID=BECKE Use Becke partition + bragg radius
[x] Checkpoint File: -LCHECK Do not perform SCF but load info from checkpoint -SCHECK Save checkpoint file at the end (default=no) -SCHECK=ALL Save checkpoint file every scf cycle (default=no) -FCHECK=STR Set file name for checkpoint (default=checkpoint.txt) -LDMATRIX Load density matrix at the beginning (default=no) -SDMATRIX Save density matrix at the end (default=no) -FDMATRIX=STR Set file name for density matrix (default=dmatrix.txt)
[x] Output: -DENSITY Print electron density volume information -POTENTIAL Print electric potential volume information -GRADOVER43 Gradient over rho^4/3 volume information -GRADRS Gradient electron radius volume information -MOUP=INT Print spin up mo. volume info (index starts at 1) -MODN=INT Print spin dn mo. volume info (index starts at 1) -VOLCUT=REAL Set accuracy for computing volume info (default=1.0E-4) -VOLGRID=INT Set the number of grid points per angstrom (default=10) -XSF Volume info. will be in XSF format to 'volume.xsf' -CUBE Volume info. will be in CUBE format to 'volume.cube' -GAUSSIAN Emulate Gaussian output to 'gaussian.log' (for GabEdit)
[x] Parallel Run: -NCPU=INT Set the number of CPUs (default=1) -PREFIX=STR Set prefix string for the job (default=SQ)
[x] Geometry Optimization: -OPTMAX=INT Maximum number of iterations (default=30)
[x] Minimum Energy Crossing Point (MECP): -MECPMAX=INT Maximum number of iterations (default=30) -FCHECKA=STR State A checkpoint file name (default=checkpointA.txt) -FCHECKB=STR State B checkpoint file name (default=checkpointB.txt) -FDMATRIXA=STR State A density matrix file name (default=dmatrixA.txt) -FDMATRIXB=STR State B density matrix file name (default=dmatrixB.txt) -GAUSSINA=STR State A Gaussian input file name (excluding .com) -GAUSSINB=STR State B Gaussian input file name (excluding .com) -GAUSSEXE=STR Gaussian program execution string
[x] External Field: -EF=EX,EY,EZ Uniform electric field in AU (default=0.0,0.0,0.0) Electric field 1 AU = 51.4220652 Volt/Angstrom
[x] Quantum Molecular Dynamics (QMD): -INITVEL=STR Initial velocity from the file in xyz format (nm/ps) -INITTEMP=REAL Initial velocity at random using the temp. (kelvin) -KEEPTEMP=REAL Rescale velocity to maintain the temp. (default=none) -TRAJ=STR Set output trajectory file (default=traj.xyz) -DT=REAL Set time step in pico-sec (default=0.001) -QMDMAX=INT Set maximum number of steps (default=25) -EFREQ=REAL Set electric field frequency in THz (default=0.0)
[x] Some of available functionals from LIBXC: XC_LDA_C_2D_AMGB XC_LDA_C_BR78 XC_LDA_C_CHACHIYO XC_LDA_C_GL XC_LDA_C_HL XC_LDA_C_LP_A XC_LDA_C_LP_B XC_LDA_C_MCWEENY XC_LDA_C_ML1 XC_LDA_C_ML2 XC_LDA_C_OB_PW XC_LDA_C_OB_PZ XC_LDA_C_OW XC_LDA_C_OW_LYP XC_LDA_C_PK09 XC_LDA_C_PW XC_LDA_C_PW_MOD XC_LDA_C_PW_RPA XC_LDA_C_PZ XC_LDA_C_PZ_MOD XC_LDA_C_RC04 XC_LDA_C_vBH XC_LDA_C_VWN XC_LDA_C_VWN_1 XC_LDA_C_VWN_2 XC_LDA_C_VWN_3 XC_LDA_C_VWN_4 XC_LDA_C_VWN_RPA XC_LDA_C_XALPHA XC_LDA_K_LP XC_LDA_K_TF XC_LDA_K_ZLP XC_LDA_X XC_LDA_X_1D XC_LDA_X_2D XC_LDA_X_ERF XC_LDA_X_RAE XC_LDA_X_REL XC_LDA_XC_GDSMFB XC_LDA_XC_KSDT XC_LDA_XC_TETER93 XC_GGA_C_AM05 XC_GGA_C_APBE XC_GGA_C_BCGP XC_GGA_C_BMK XC_GGA_C_FT97 XC_GGA_C_GAM XC_GGA_C_GAPLOC XC_GGA_C_HCTH_A XC_GGA_C_LM XC_GGA_C_LYP XC_GGA_C_N12 XC_GGA_C_N12_SX XC_GGA_C_OPTC XC_GGA_C_OP_B88 XC_GGA_C_OP_PW91 XC_GGA_C_OP_PBE XC_GGA_C_P86 XC_GGA_C_PBE XC_GGA_C_PBEFE XC_GGA_C_PBEINT XC_GGA_C_PBELOC XC_GGA_C_PBE_JRGX XC_GGA_C_PBE_MOL XC_GGA_C_PBE_SOL XC_GGA_C_PW91 XC_GGA_C_Q2D XC_GGA_C_REGTPSS XC_GGA_C_RGE2 XC_GGA_C_SCAN_E0 XC_GGA_C_SG4 XC_GGA_C_SOGGA11 XC_GGA_C_SOGGA11_X XC_GGA_C_SPBE XC_GGA_C_TAU_HCTH XC_GGA_C_TCA XC_GGA_C_TM_PBE XC_GGA_C_TM_LYP XC_GGA_C_W94 XC_GGA_C_WI0 XC_GGA_C_WI XC_GGA_C_WL XC_GGA_C_XPBE XC_GGA_C_ZPBEINT XC_GGA_C_ZPBESOL XC_GGA_C_ZVPBEINT XC_GGA_C_ZVPBESOL XC_GGA_K_ABSP1 XC_GGA_K_ABSP2 XC_GGA_K_ABSP3 XC_GGA_K_ABSP4 XC_GGA_K_BALTIN XC_GGA_K_DK XC_GGA_K_ERNZERHOF XC_GGA_K_GE2 XC_GGA_K_GOLDEN XC_GGA_K_GP85 XC_GGA_K_GR XC_GGA_K_LIEB XC_GGA_K_LUDENA XC_GGA_K_MEYER XC_GGA_K_OL2 XC_GGA_K_TFVW XC_GGA_K_VJKS XC_GGA_K_VSK XC_GGA_K_VW XC_GGA_K_YT65 XC_GGA_X_FT97_A XC_GGA_X_FT97_B XC_GGA_X_GAM XC_GGA_X_HERMAN XC_GGA_X_HJS_B88 XC_GGA_X_HJS_B88_V2 XC_GGA_X_HJS_B97X XC_GGA_X_HJS_PBE XC_GGA_X_HJS_PBE_SOL XC_GGA_X_HTBS XC_GGA_X_KT1 XC_GGA_X_N12 XC_GGA_X_OL2 XC_GGA_X_SOGGA11 XC_GGA_X_SSB XC_GGA_X_SSB_D XC_GGA_X_VMT84_GE XC_GGA_X_VMT84_PBE XC_GGA_X_WPBEH XC_GGA_XC_B97_D XC_GGA_XC_B97_GGA1 XC_GGA_XC_BEEFVDW XC_GGA_XC_EDF1 XC_GGA_XC_HCTH_120 XC_GGA_XC_HCTH_147 XC_GGA_XC_HCTH_407 XC_GGA_XC_HCTH_407P XC_GGA_XC_HCTH_93 XC_GGA_XC_HCTH_P14 XC_GGA_XC_HCTH_P76 XC_GGA_XC_HLE16 XC_GGA_XC_KT1 XC_GGA_XC_KT2 XC_GGA_XC_MOHLYP XC_GGA_XC_MOHLYP2 XC_GGA_XC_MPWLYP1W XC_GGA_XC_OBLYP_D XC_GGA_XC_OPBE_D XC_GGA_XC_OPWLYP_D XC_GGA_XC_PBE1W XC_GGA_XC_PBELYP1W XC_GGA_XC_TH1 XC_GGA_XC_TH_FL XC_GGA_XC_XLYP XC_MGGA_C_B88 XC_MGGA_C_DLDF XC_MGGA_C_KCIS XC_MGGA_C_M05 XC_MGGA_C_M05_2X XC_MGGA_C_M06 XC_MGGA_C_M06_2X XC_MGGA_C_M06_HF XC_MGGA_C_M06_L XC_MGGA_C_PKZB XC_MGGA_C_REVTPSS XC_MGGA_C_TPSS XC_MGGA_C_TPSSLOC XC_MGGA_X_M11 XC_MGGA_X_M11_L XC_MGGA_X_MBEEF XC_MGGA_X_MBEEFVDW XC_MGGA_X_MK00B XC_MGGA_X_TM XC_MGGA_X_VT84 XC_MGGA_XC_B97M_V XC_MGGA_XC_OTPSS_D XC_MGGA_XC_TPSSLYP1W Program status The current package contains Siam Quantum binaries of version 1.2.14 compiled for the particular hardware platforms. License Siam Quantum This distribution is published as freeware at Mobile Chemistry Portal and Google Play Store with kind permission of Teepanis Chachiyo. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. The basis files were taken from the Basis Set Exchange Portal (GAMESS-US style). MinGW The Windows version contains unix2dos binary which is a part of MinGW runtime.
Copyright (c) 2012 MinGW.org project BLAS Siam Quantum binaries offered by us were statically linked to BLAS library (freely-available software package, available in the homepage). LAPACK Siam Quantum binaries offered by us were statically linked to LAPACK library (released under modified BSD license, check the homepage for details). LibXC Siam Quantum binaries offered by us were statically linked to LibXC library (released under the MPL license (v. 2.0), check the homepage for details). Note: The 32-bit versions of SiamQuantum were compiled without support for mgga_x_2d_prhg07 functional due to cross-compiler issues. X11-Basic GUI of the Windows version was built using X11-Basic (by Markus Hoffmann) framework (GPL v.3). For correct functionality, SDL library (available under GNU LGPL license) is included in package. Advanced Installer The MSI installer for Windows was created using the Advanced Installer (Freeware edition). Distribution (A) Self-extracting installers with graphical user interface (recommended for most users)
(B) Binaries and corresponding documentation (for advanced users) Android up to 4.4 (Kitkat) (obsolete) In case of your interest, please contact us by e-mail. Android 5.0 (Lollipop) und later (position independent executables)
Windows version
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