RedS software

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RedS

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RedS is a user-friendly program for output parsing, atomic coordinate conversion, and vibrational and geometry optimization data manipulation.

With RedS, you can

monitor interatomic distances/angles, S², and the SCF energy during geometry optimizations

monitor changes in internuclear distances (vibrational frequency calculations)

shift the atomic coordinate origin

a parallel shift by a specified (x,y,z)
put (0,0,0) at a specified atom
put (0,0,0) between specified atoms (two or more)

rotate the coordinate system

using Euler angles

rescale or/and format atomic coordinates

exchange X, Y, Z

write atomic coordinates as

a standard XYZ file
a Hyperchem HIN file (HyperCube, Inc.)
a symbolic XYZ matrix for a partial optimization with Gaussian 98/03 (Gaussian, Inc.)

RedS also creates summary reports (those can include multiple items: method of calculation, molecular composition, total energy, frontier orbital energies, HOMO-LUMO gaps, MPA and NPA charges and spin densities of the user-specified atoms, user-specified bond distances and angles, molecular geometry/charge descriptor, etc.) from Gaussian 98/03 output files.

An example of an instruction file (*.DES) for RedS is given below:

# This is an example of a RedS descriptor file. # You can include comment lines in the beginning if the file. # These lines should contain the # character and will be ignored by the program. # GEOMETRY 2 1 28 2 1 2 2 1 4 2 1 6 3 1 28 29 0 WATCH ATOMS 1 2 4 6 28 0 ADD 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 0 IONIC 28 ---- SEARCH ---- up to 10 statements ----- Stoichiometry Output= Error termination ------------------------------------------

These instrictions tell RedS to:

monitor the interactomic distances between atom 1 and atom 28, atom 1 and atom 2, atom 1 and atom 4, atom 1 and atom 6, and the interatomic angle between atoms 1, 28, and 29 (the GEOMETRY keyword);

monitor atomic charges (MPA, NPA and other applicable charge schemes) and spin densities (MPA, NPA) of atoms 1, 2, 4, 6, and 28 (the WATCH ATOMS keyword);

add atomic charges (MPA, NPA and all other applicable charge schemes) and spin densities (MPA, NPA) of atoms 2-27 together and print the corresponding sums (the ADD keyword);

calculate the electrostatic interaction between two fragments of a molecule as a sum q_i * q_j / r_ij (i=1-27 and j=28-to the end of the molecule), where r_ij are interatomic distances and q_i are NPA atomic charges (the IONIC keyword, the first atom of the second fragment (atom 28 in the above example) defines the molecule partitioning into the two fragments) (refer to Inorg. Chem. 2005, 44, pp 4947 - 4960 [PDF] for details);

print all lines which contain user-selected statements such as Error termination and Stoichiometry (the SEARCH keyword).

An example of a summary file (*.SUM) is given below (this summary report has been created using the instruction file shown above on this page):

Output=MC-F1F2-SC6F5-Cu-symm-B3LYP-TZVP-S.log %chk=Cu-F1F2-symm-B3LYP-TZall #P B3LYP/TZVP 5D Test Guess=Check SCF=Tight IOp(3/33=1) Pop=(Full,NPA)Geom=Check Stoichiometry C15H10BCuF5N6S(2) 628 basis functions, 1158 primitive gaussians, 659 cartesian basis functions 1-SCF= -3469.500504 DeltaSCF= 0.8339 eV E-SCF= -3469.531152 a.u. S**2= 0.756 Descriptor= 0.00 Alpha HOMO= -6.5743 LUMO= -1.1611 Gap= 5.4132 eV Beta HOMO= -6.6279 LUMO= -4.2385 Gap= 2.3895 eV ---- NPA-derived numbers ---- Sum q(i)q(j)/R(ij): -402.9 kcal/mol Sum q(i)q(j)/R(ij) between the fragments -29 kcal/mol Fragment 1: -292.4 kcal/mol Fragment 2: -81.5 kcal/mol --- GEOMETRY --- 1-28 1-2 1-4 1-6 1-28-29 2.204 2.230 2.015 2.015 113.2 --- WATCHED ATOMS --- Cu(1) N(2) N(4) N(6) S(28) 2+3+4+5+6+7+8+9+10+11+12+13+14+15+16+17+18+19+20+21+22+23+24+25+26+27 q(MPA): 0.107 -0.023 0.044 0.044 -0.013 0.047 q(NPA): 1.144 -0.385 -0.381 -0.381 -0.207 -0.697 s(MPA): 0.472 0.000 0.071 0.071 0.309 0.140 s(NPA): 0.480 -0.001 0.073 0.073 0.300 0.143

In the first section of the summary, RedS prints

the name of checkpoint file for this calculation,
the first Gaussian command line (#P)
stoichiometry and basis set information,
total energy and the S² value,
the energies of aplha-spin HOMO and LUMO, and the corresponding energy gap,
(if spin-unrestricted calculation) the energies of beta-spin HOMO and LUMO, and the corresponding energy gap,
the sum q_i * q_j / r_ij for all atom pairs, where r_ij are interatomic distances and q_i are NPA atomic charges.
the sum q_i * q_j / r_ij for all atom pairs, where r_ij are interatomic distances and q_i are electrostatic potential-derived atomic charges.

If RedS is executed with a Gaussian 98/03 optimization output file, RedS prints a summary report (*.SCF) for the optimization:

Opt ITER SCF Energy Watched Parameter(s) Step (a.u.) S**2 1-5 2-5 3-5 4-5 1-5-2 3-5-4 1-71 4-71 69-70 70-71 69-70-71 1 46 -8728.7715086 0.81 2.447 2.438 2.366 2.216 167.5 76.4 3.610 2.119 1.213 1.322 139.5 2 28 -8728.8084617 0.76 2.457 2.425 2.354 2.206 168.0 76.8 3.568 2.121 1.164 1.280 141.8 3 23 -8728.8199499 0.76 2.482 2.393 2.316 2.185 169.1 78.2 3.563 2.142 1.135 1.235 147.9 4 23 -8728.8263434 0.76 2.519 2.353 2.272 2.166 169.9 80.0 3.590 2.187 1.128 1.200 156.0 5 22 -8728.8314759 0.76 2.560 2.321 2.251 2.159 170.3 81.4 3.633 2.259 1.126 1.185 164.5 6 23 -8728.8355730 0.76 2.630 2.280 2.232 2.155 170.2 83.5 3.709 2.418 1.123 1.178 178.1 7 19 -8728.8373073 0.76 2.635 2.290 2.242 2.160 170.1 83.7 3.736 2.467 1.128 1.187 177.6 8 23 -8728.8388368 0.76 2.635 2.306 2.248 2.167 169.7 83.9 3.764 2.534 1.129 1.189 175.7 9 22 -8728.8399402 0.76 2.640 2.328 2.246 2.176 168.5 84.7 3.827 2.693 1.127 1.185 174.0 10 23 -8728.8406517 0.76 2.641 2.329 2.235 2.176 168.0 85.2 3.858 2.761 1.125 1.182 174.7 11 18 -8728.8410385 0.76 2.635 2.326 2.227 2.173 167.9 85.4 3.876 2.788 1.126 1.183 175.1 12 23 -8728.8414458 0.76 2.616 2.325 2.215 2.167 167.8 85.7 3.915 2.855 1.125 1.181 175.7 13 24 -8728.8418268 0.76 2.581 2.327 2.211 2.161 167.9 85.8 3.961 2.930 1.125 1.179 175.9 14 22 -8728.8422919 0.76 2.516 2.335 2.210 2.153 168.3 85.8 4.035 3.044 1.125 1.179 176.0 15 22 -8728.8429122 0.76 2.447 2.347 2.218 2.150 168.8 85.5 4.096 3.137 1.126 1.178 176.2 16 22 -8728.8436993 0.76 2.368 2.364 2.235 2.154 169.6 85.0 4.142 3.209 1.125 1.177 176.8 17 23 -8728.8440807 0.76 2.333 2.373 2.243 2.158 169.7 85.1 4.155 3.234 1.125 1.178 177.2 18 20 -8728.8443248 0.76 2.324 2.375 2.243 2.160 169.4 85.5 4.160 3.249 1.126 1.178 177.4 19 23 -8728.8446368 0.76 2.306 2.376 2.237 2.160 168.4 86.4 4.181 3.304 1.126 1.178 177.8 20 24 -8728.8448437 0.76 2.308 2.373 2.228 2.159 167.5 87.3 4.195 3.347 1.126 1.177 178.0 21 23 -8728.8450102 0.76 2.300 2.371 2.219 2.156 166.3 88.4 4.226 3.422 1.127 1.177 178.0 22 30 -8728.8451344 0.76 2.308 2.368 2.213 2.154 165.4 89.2 4.247 3.482 1.126 1.175 178.2 23 23 -8728.8452539 0.76 2.299 2.368 2.211 2.151 164.9 89.7 4.277 3.550 1.126 1.175 178.1 24 18 -8728.8453936 0.76 2.304 2.367 2.212 2.149 164.6 90.1 4.304 3.619 1.126 1.175 178.1 25 22 -8728.8455262 0.76 2.294 2.369 2.218 2.147 164.6 90.3 4.343 3.715 1.126 1.175 178.0 26 23 -8728.8456508 0.76 2.302 2.368 2.223 2.147 164.8 90.4 4.361 3.779 1.125 1.175 178.1 27 23 -8728.8458266 0.76 2.294 2.369 2.231 2.148 165.2 90.3 4.384 3.865 1.126 1.175 178.0 28 23 -8728.8460466 0.76 2.306 2.365 2.238 2.150 166.0 90.3 4.392 3.953 1.126 1.174 178.4 29 23 -8728.8462948 0.76 2.305 2.363 2.240 2.152 166.6 90.2 4.392 4.023 1.126 1.174 178.5 30 22 -8728.8466099 0.76 2.317 2.357 2.239 2.154 167.3 90.3 4.379 4.125 1.126 1.173 179.0 31 22 -8728.8468678 0.76 2.324 2.352 2.232 2.156 167.6 90.4 4.366 4.223 1.127 1.173 179.2

Here the 1st column indicates the optimization step, the second column is the number of SCF iterations it took to reach the convergence, the 3rd column is the SCF energy, the 4th column is the S² value, and the remaining columns indicate the values of the watched parameters (interatomic distances and angles) as specified by a user in the RedS instruction file.

If RedS is executed with a Gaussian 98/03 frequency output file (the FREQ or OPT=CALCALL keywords in Gaussian), RedS prints a summary report for the calculated normal modes. This report contains normal mode frequencies (cm^-1), IR intensities, and changes in the interatomic distances of user-defined atomic pairs. For example:

Vibrational Data # cm(-1) I(IR) Internuclear distance variations (A) 1-28 1-2 1-4 1-6 1 -7.2 0.0 0.00 0.00 0.00 0.00 2 12.7 0.1 0.00 0.00 0.00 0.01 3 22.3 0.0 0.00 0.01 0.00 0.00 4 47.2 0.5 0.01 0.00 0.01 0.00 5 50.0 0.6 0.01 -0.03 0.00 0.00 6 54.7 0.3 0.01 0.00 0.00 0.00 7 71.7 0.1 0.02 -0.04 0.00 0.00 8 83.3 0.5 0.00 0.02 0.01 0.00 9 111.6 0.3 0.06 0.01 -0.05 0.05 10 115.5 0.8 0.13 0.13 0.05 0.05 11 130.7 0.0 0.00 0.00 -0.01 0.01 12 137.0 0.3 0.00 0.01 -0.03 0.04 13 137.5 4.5 -0.03 0.34 -0.07 -0.07 14 152.6 0.0 0.00 0.00 0.03 -0.02 15 162.1 14.7 -0.03 0.22 0.02 0.02 16 168.4 0.1 0.00 0.00 -0.07 0.07 17 203.8 6.7 0.01 0.03 -0.13 -0.13 18 205.6 2.4 0.02 0.03 -0.27 0.31 19 216.7 14.1 0.03 0.02 -0.25 0.28 20 228.0 13.4 -0.06 0.11 0.18 0.18 21 276.8 0.4 0.04 0.03 -0.01 -0.01 22 277.2 0.3 0.00 0.00 0.03 0.00 23 278.3 0.2 -0.02 0.03 0.04 0.04 24 281.3 0.9 -0.02 0.00 0.00 0.00 25 311.4 11.5 -0.13 -0.06 0.04 0.04 26 312.8 1.1 0.00 0.01 0.00 0.00 27 329.9 2.1 0.00 0.01 -0.11 0.11 28 332.7 2.2 -0.03 -0.13 0.02 0.02 29 341.7 2.1 0.24 0.07 0.12 0.12 30 361.1 0.9 0.00 0.00 -0.03 0.03 31 364.9 57.4 -0.41 0.14 0.25 0.25 32 384.9 0.0 0.00 0.00 0.00 0.00 33 408.6 5.8 0.67 -0.06 -0.16 -0.16 34 447.4 1.1 -0.13 0.00 0.02 0.02 35 515.3 0.1 0.18 -0.01 -0.01 -0.01 ...

Interatomic distance changes for normal modes are reported for atom pairs that are listed in a descriptor file (in the above example, these are: atoms 1 and 18, 1 and 2, 1 and 4, and 1 and 6). This RedS summary allows a user to select and analyze normal modes of interest.

Current program limitations:

The maximum number of atoms: 1000.

The maximum number of atoms in the descriptor file lists (WATCHED ATOMS, watched structural parameters, etc.): 50.


	RedS processes output files from the following QC programs:

	Gaussian 98/03 (Gaussian, Inc.)
	XYZ files

Operating System: Windows 2000/XP

System Requirements: PC with Pentium-II (or higher) processor.


	The RedS program can be obtained as part of the AOMix site license. If you would like to obtain the program, please follow these instructions.

WWW.SG-CHEM.NET
All contents copyright � 1997-2010 S. I. Gorelsky
Last updated: January 2010

Operating System:	Windows 2000/XP
System Requirements:	PC with Pentium-II (or higher) processor.