PAMoC Tutorials

Tutorial 1: atom coordinates as only input data

This tutorial shows what PAMoC can do when you know only the structure of a molecule. In the following example we use a “shell script”, which comprises a series of command for the shell to execute. A shell script can combine lengthy and repetitive sequences of commands into a single and simple script, which can be stored and executed anytime, so reducing the effort required by the end user. The script starts with the shebang operator “#!” which directs the script to the interpreter location. Since the example uses “#!/bin/sh” the script gets directed to the bourne-shell. The command on the second line of the script launches the PAMoC executable code “pamoc.exe” and redirects the standard input as a “here-document”, i.e. it instructs the shell (“<< EOF”) to read input from the current source until a line containing only the delimiter “EOF” (with no trailing blanks) is seen. In addition the standard output and the standard error are redirected (“>&”) to the file “pamoc.out”. The PAMoC data input in the following script comprises the option for debugging, a title and the atom coordinatesInput of atom coordinates
(click to display the page in a separate tab). Atom coordinates are not given explicitly, but using an attached file, which is specified by its pathname prepended with an at sign (@). Rules for specifying atom coordinates are descibed in the “Data Input”Data Input: 2. − Atom coordinates
(click to display the page in a separate tab) section of the manual.

#!/bin/sh pamoc.exe << EOF >& pamoc.out debug alpha-glycine at the experimental x-ray geometry (23 K) COORD ANGSTROM @/home/barzaghi/src/pamoc/tests/gly/interfaces/gly-expgeo.xyz END EOF

Assuming that the shell script is saved as file gly.sh, for executing the script type

bash gly.sh

At the beginning of the printout file (pamoc.out) you will find an image of data input, including the content of the attached file. It is followed by a list of the options with their default values, and of the environment variables. Then, a warning is reported because no interface data file has been provided. Finally, a list of the actions taken by PAMoC in its initialization step is reported.

pamoc.exe was invoked by barzaghi@barzaghi-desktop Tue 25-Sep-2018 22:58:52 ******************************************************************************* PAMOC RV 2014-03-01 PAMOC Properties of Atoms in Molecules and Crystals from Experimental and Theoretical Charge Densities mario.barzaghi@cnr.it https://www.pamoc.it ******************************************************************************* Data input taken from standard input. AtFile(1): /home/barzaghi/src/pamoc/tests/gly/interfaces/gly-expgeo.xyz debug alpha-glycine at the experimental x-ray geometry (23 K) COORD ANGSTROM C1 0.2182 1.47356 0.33304 C2 0.73246 1.71712 -1.08363 N1 2.03095 1.04051 -1.31397 O1 1.05323 1.10421 1.19684 O2 -1.00741 1.67621 0.5394 H1 2.3379 1.18084 -2.29262 H2 2.75764 1.37745 -0.67714 H3 1.93566 0.03426 -1.14702 H4 0.87485 2.7781 -1.22321 H5 0.01335 1.35273 -1.81742 END End of data from standard input. Debug Output File: fort.99 Options: IPrint 9 Debug T Interface (stop after) F Moments (stop after) F ECryst (stop after) F NoECryst F TopologyOnly F UseTopo2 F Grid F ChkTopo2F F UseSymmetry F Crystal F ChargeNorm F Bohr F NoVariance F DiagVCMatrix F DbgNuMom F DFT F Export DMA F NoMolRec F ScalePop F NoElProp F NoCrystalTop F Include Loose Hydrogen Bonds F READ TOPology from disk file F SAVE TOPology on disk file F QTAIM partitioning F EP/MM F E_Cryst extended Printing F lmx 4 Integration Grid Selection 11 Moment Origin 0 UseDMA 0 CluDim 1 MaxErr 3 Atoms to be integrated (QTAIM) 0 Dimer 0 E_Cryst Model 2 Atomic Repulsion Parameters 5 Atomic Dispersion Parameters 5 Damping Function for Dispersion 4 Modify Density Basis Set 0 EPMM Penetration Threshold J/mol 500 Moment shift procedure (0|1|2|3) 2 Molecular moments printing optns 2213 Radial quadrature rule 31 Standardization of Radial Grid 0 Order of Knowles Grid 3 Order of Handy Grid 2 Definition of covalent radii 0 DMA printing options 10011 Environment Variables: USER barzaghi PWD /home/barzaghi TERM xterm-256color DISPLAY :0 WARNING: the Interface Data File (IDF) is missing.

The next page reports a list of the actions taken by PAMoC in the initialization step.

******************************************************************************* PAMOC RV 2014-03-01 PAMOC Initialization of Data from Input- and Interface-data files mario.barzaghi@cnr.it https://www.pamoc.it ******************************************************************************* Cell constants, Symmetry operations, etc. ... done Atom sites in the crystal/molecule ... done Symmetry ... done Density Basis Set ... done
×Notice: The text in the
green box on the left
is only printed if   IPrint ≥ 2.
Evaluation of Atomic Charges by the Electronegativity Equalization Method ------------------------------------------------------------------------- EEM parameters A and B with kappa = 0.44, and estimated atomic charges ------------------------------------------------------------------------- I Element A B Atomic Charge ------------------------------------------------------------------------- 1 6 C 2.459 0.611 0.274 2 6 C 2.459 0.611 -0.054 3 7 N 2.597 0.790 -0.461 4 8 O 2.625 0.858 -0.263 5 8 O 2.625 0.858 -0.262 6 1 H 2.396 0.959 0.174 7 1 H 2.396 0.959 0.194 8 1 H 2.396 0.959 0.191 9 1 H 2.396 0.959 0.103 10 1 H 2.396 0.959 0.103 ------------------------------------------------------------------------- Electronegativity Equalization Method: Parameterization and Validation for Large Sets of Organic, Organohalogene and Organometal Molecule Radka Svobodova Varekova, Zuzana Jirouskova, Jakub Vanek, Simon Suchomel, and Jaroslav Koca, Int. J. Mol. Sci. 2007, 8, 572-582.
EEM populations ... done Spherical Atom Model with partial atomic charges estimated by the Electronegativity Equalization Method (EEM). Nuclear Centred Multipole Moments ... done Evaluation of molecular descriptors ... done Initialization Step cpu time: 0.0 seconds. Common /DMAStat/ IStatDMA(0:MxDMA) : 9 0 0 0 0 0 0 0 0 111 default dma 9 dma 1 F dma 2 F dma 3 F dma 4 F dma 5 F dma 6 F dma 7 F dma 8 F dma 9 T 1 -0.73522 0.11761 0.66754 0.70516 0.60714 -0.32361 0.72571 1.38486 0.30138 0.93885 0.16652 -0.17422 ******************************************************************************* PAMOC RV 2014-03-01 PAMOC Information on the Molecular System ----------------------------------- mario.barzaghi@cnr.it https://www.pamoc.it ******************************************************************************* ---------------------------------------------------------------------------- IDF reference system with origin at x=0, y=0, z=0 ---------------------------------------------------------------------------- Center Center Atomic Coordinates (Angstroms) Atomic Net Charge Number Label Number X Y Z EEM ---------------------------------------------------------------------------- 1 C1 6 0.218200 1.473560 0.333040 0.274 2 C2 6 0.732460 1.717120 -1.083630 -0.054 3 N1 7 2.030950 1.040510 -1.313970 -0.461 4 O1 8 1.053230 1.104210 1.196840 -0.263 5 O2 8 -1.007410 1.676210 0.539400 -0.262 6 H1 1 2.337900 1.180840 -2.292620 0.174 7 H2 1 2.757640 1.377450 -0.677140 0.194 8 H3 1 1.935660 0.034260 -1.147020 0.191 9 H4 1 0.874850 2.778100 -1.223210 0.103 10 H5 1 0.013350 1.352730 -1.817420 0.103 ---------------------------------------------------------------------------- Center of Mass 0.647213 1.387502 -0.091282 Center of Charges 0.705164 1.384860 -0.174221 Molecular Charge 0.000 Total number of electrons 40.000 Multiplicity 1 Point Group C1 Stoichiometry C2H5NO2(0) Principal Moments of Inertia: 48.8539 128.1109 169.0955 (amu-Angstrom**2) Anisotropy: 105.8760 (amu-Angstrom**2) Asphericity (relative anisotropy): 0.3059 Largest atomic distance from the center of mass: 2.7833 (Angstrom) --------------------------------------------------------- Translated and Rotated Cartesion Coordinates (Angstroms) --------------------------------------------------------- Origin: center of mass Reference System: principal axes of the inertial tensor --------------------------------------------------------- Center Center Atomic Coordinates (Angstroms) Number Label Number X Y Z --------------------------------------------------------- 1 C1 6 0.608512 -0.025092 -0.024324 2 C2 6 -0.680410 0.778777 -0.176682 3 N1 7 -1.874377 -0.047679 0.120549 4 O1 8 0.516908 -1.278232 -0.057370 5 O2 8 1.677350 0.627452 0.108121 6 H1 1 -2.732210 0.528154 0.055693 7 H2 1 -1.953273 -0.849156 -0.510775 8 H3 1 -1.810692 -0.425553 1.070626 9 H4 1 -0.754563 1.125135 -1.196473 10 H5 1 -0.674393 1.638241 0.493865 --------------------------------------------------------- Center of Mass 0.000000 0.000000 0.000000 Center of Charges -0.098077 0.024973 -0.001081 Euler angles (degree): Alpha = 219.184, Beta = 16.918, Gamma = 260.358 | -0.742 0.117 0.661| Rotation Matrix = | -0.604 0.311 -0.733| | -0.291 -0.943 -0.160| ******************************************************************************* PAMOC RV 2014-03-01 PAMOC Molecular Electrostatic Multipole Moments (unabridged cartesian tensors) obtained from different DMA of the electron density Standard units: electrons, Debye, Debye-Ang, Debye-Ang**2, Debye-Ang**3 Origin: Center of Mass - Reference System: principal axes of the inertial ten mario.barzaghi@cnr.it https://www.pamoc.it ******************************************************************************* ------------------------------------- L <O> EEM ------------------------------------- 1 0 0 <q> 0.0000 2 1 1 <x> -4.1115 3 1 2 <y> 1.3262 4 1 3 <z> -0.1128 Dipole 4.3216 5 2 1 <xx> 2.0339 6 2 2 <xy> -0.4942 7 2 3 <yy> 0.3119 8 2 4 <xz> -0.4307 9 2 5 <yz> -0.3793 10 2 6 <zz> 2.0650 (<xx> + <yy> + <zz>)/3 1.4703 Anisotropy 1.4756 11 3 1 <xxx> -20.9900 12 3 2 <yyy> 4.5728 13 3 3 <zzz> 0.2094 14 3 4 <xyy> -5.4050 15 3 5 <xxy> -1.8347 16 3 6 <xxz> 0.2249 17 3 7 <xzz> -2.9583 18 3 8 <yzz> 0.3330 19 3 9 <yyz> -0.1512 20 3 10 <xyz> -0.1111 <xxx> + <xyy> + <xzz> -29.3533 <yyy> + <xxy> + <yzz> 3.0711 <zzz> + <xxz> + <yyz> 0.2831 Magnitude of vector part 29.5149 Project. on dipole dir. 28.8615 21 4 1 <xxxx> 33.1224 22 4 2 <yyyy> 1.2882 23 4 3 <zzzz> 2.3067 24 4 4 <xxxy> -5.4357 25 4 5 <xxxz> -1.9320 26 4 6 <yyyx> -0.1717 27 4 7 <yyyz> 0.2968 28 4 8 <zzzx> -1.1899 29 4 9 <zzzy> -1.2258 30 4 10 <xxyy> 3.7850 31 4 11 <xxzz> 4.6873 32 4 12 <yyzz> 1.5687 33 4 13 <xxyz> -0.0374 34 4 14 <yyxz> 0.3889 35 4 15 <zzxy> 0.4635 <xxxx> + <xxyy> + <xxzz> 41.5947 <yyyy> + <xxyy> + <yyzz> 6.6418 <zzzz> + <yyzz> + <xxzz> 8.5627 <xxxy> + <yyyx> + <zzxy> -5.1439 <xxxz> + <zzzx> + <yyxz> -2.7330 <yyyz> + <zzzy> + <xxyz> -0.9664 Isotropic value 18.9331 ------------------------------------- ******************************************************************************* PAMOC RV 2014-03-01 PAMOC Molecular Electrostatic Multipole Moments (traceless cartesian tensors) obtained from different DMA of the electron density Standard units: electrons, Debye, Debye-Ang, Debye-Ang**2, Debye-Ang**3 Origin: Center of Mass - Reference System: principal axes of the inertial ten mario.barzaghi@cnr.it https://www.pamoc.it ******************************************************************************* ------------------------------------- L <O> EEM ------------------------------------- 1 0 0 <q> 0.0000 2 1 1 <x> -4.1115 3 1 2 <y> 1.3262 4 1 3 <z> -0.1128 Dipole 4.3216 5 2 1 <xx> 0.8455 6 2 2 <xy> -0.7413 7 2 3 <yy> -1.7376 8 2 4 <xz> -0.6460 9 2 5 <yz> -0.5690 10 2 6 <zz> 0.8921 Anisotropy 1.8072 11 3 1 <xxx> -8.4451 12 3 2 <yyy> 6.8254 13 3 3 <zzz> 0.0989 14 3 4 <xyy> 1.1642 15 3 5 <xxy> -6.1224 16 3 6 <xxz> 0.4207 17 3 7 <xzz> 7.2809 18 3 8 <yzz> -0.7030 19 3 9 <yyz> -0.5196 20 3 10 <xyz> -0.2776 21 4 1 <xxxx> 10.2302 22 4 2 <yyyy> 2.0288 23 4 3 <zzzz> -0.7185 24 4 4 <xxxy> -14.1364 25 4 5 <xxxz> -3.3279 26 4 6 <yyyx> 8.8935 27 4 7 <yyyz> 3.1107 28 4 8 <zzzx> -0.0815 29 4 9 <zzzy> -3.5509 30 4 10 <xxyy> -6.4888 31 4 11 <xxzz> -3.7415 32 4 12 <yyzz> 4.4599 33 4 13 <xxyz> 0.4402 34 4 14 <yyxz> 3.4094 35 4 15 <zzxy> 5.2429 ------------------------------------- ******************************************************************************* PAMOC RV 2014-03-01 PAMOC Molecular Electrostatic Multipole Moments (spherical tensors) obtained from different DMA of the electron density Standard units: electrons, Debye, Debye-Ang, Debye-Ang**2, Debye-Ang**3 Origin: Center of Mass - Reference System: principal axes of the inertial ten mario.barzaghi@cnr.it https://www.pamoc.it ******************************************************************************* -------------------- <L, M> EEM -------------------- <0, 0> 0.0000 <1,+1> -4.1115 <1,-1> 1.3262 <1, 0> -0.1128 <2, 2> 5.1661 <2,-2> -2.9652 <2, 1> -1.2921 <2,-1> -1.1379 <2, 0> 0.8921 <3, 3> -71.6253 <3,-3> -151.1552 <3, 2> 5.6420 <3,-2> -3.3315 <3, 1> 21.8428 <3,-1> -2.1090 <3, 0> 0.0989 <4, 4> 1228.5979 <4,-4> -2210.8640 <4, 3> -325.3474 <4,-3> -42.9640 <4, 2> -98.4168 <4,-2> 125.8295 <4, 1> -0.3261 <4,-1> -14.2037 <4, 0> -0.7185 -------------------- Electrostatic Properties cpu time: 0.0 seconds. pamoc cpu time: 0.0 seconds. I am not a vegetarian because I love animals; I am a vegetarian because I hate plants. -- A. Whitney Brown