PQS Ab Initio Program - RELEASE 3.2 for WINDOWS
INSTALLATION
To install the PQS and/or SQM Windows software, download from the PQS Website the file pqsv32-windows.exe to any temporary directory. This file is a self-extracting zip file, and contains both the PQS quantum chemistry software and the associated Scaled Quantum Mechanical force field (SQM) vibrational program. Unlike in previous editions, there is no separate free PQS version. There is only a single PQS executable. This does not require a license up to a certain size (currently 100 basis functions and 25 atoms). Over these limits, the PQS Windows software can be run only with a license file (see below). The file pqsv32-windows.exe can be removed after installation. It is best to close all other programs before you start the PQS installation. The file pqsv32-windows.exe is a self-extracting WinZip(R) file. Double clicking on it will start WinZip which extracts and unzips the files into a temporary directory, and starts the install process. In general, you do not have to be the Administrator to install PQS. However, your system may be configured so that only the Administrator can install programs; computers used by many users are frequently set up this way. In this case, ask your system administrator for help. If the installation process fails because of file permissions, try to install as Administrator.
After unzipping the files, the setup program will bring up the installation dialogue. Only two questions need to be answered in the main dialog box:(a) the root directory (PQS_ROOT) where you wish to install PQS (e.g., C:\PQS) and (b) whether your operating system is an older version of Windows or Windows 2000 and up (Win2000 and later versions, such as Millenium and XP, behave slightly differently from earlier versions of Windows, and the install program must know if the system is Win2000). The default is Windows XP, i.e. the checkbox is unchecked. If you have an older operating system, like Windows 98, check it by clicking on it. You also have to read and accept the license agreement (see the files license.doc, license.txt or license.htm) by clicking on the accept checkbox.
Click on the "Install PQS" button to start copying the PQS files. Please wait until the installation program finishes copying files. During this time, the system copies files and it may look like it is not doing anything. When you get the "Congratulations..." screen, click OK to finish the installation and answer with yes whether you wish to exit. Make sure that your dialog boxes are not hidden under other windows; if necessary, minimize or close the latter.
If you have an earlier PQS installation, the install program will ask you if you want to overwrite it. If you are overwriting an earlier CD-ROM installation, please make sure that your files do not have the read-only attribute. If they do, the install program may not be able to overwrite them. In this case, change their attributes using Windows Explorer (select all, then right click, Properties, and uncheck Read-only).
If you want to preserve your old installation for safety, click "Cancel" in the dialog box warning that an earlier installation is present and install PQS in a different directory. (You could also rename your old PQS directory but in this case you will have to edit your old setpqs.bat script to reflect the new location of the program; i.e., if you have renamed C:\PQS to C:\PQS_OLD, you will have to exchange C:\PQS by C:\PQS_OLD in the setpqs.bat script).
After installation, please check if the contents of ALL subdirectories have been copied from the download directory to the installation directory. The reason for an incomplete installation may be twofold. The most likely reason is that your system restricts the access of users to just a few disk areas. This is possible only in the latest Windows versions, and is quite frequently employed at schools etc... to avoid the installation of unauthorized programs. Another possible reason is that Microsoft Corporation keeps making subtle changes in the command syntax.
We have checked our install program on most major Windows variants. However, if your installation is incomplete, please unzip the self-extracting install file to a temporary directory and copy the directories BASDIR, DOC, ONLINE_PQS_MAN and GAUNTLET (under the subdirectory PQS) from this temporary download directory (e.g., C:\WINDOWS\TEMP\PQS) to the install directory (say, C:\PQS). In this case, YOU WILL HAVE TO CREATE A DIRECTORY "SCR" IN YOUR PQS BASE DIRECTORY (usually C:\PQS) for the scratch files used by PQS. using Windows Explorer.
To uninstall PQS, simply delete the installation directory (e.g., C:\PQS) and all its contents (click on it and press Shift+Delete).
HARDWARE REQUIREMENTS
The code is guaranteed to run only on Intel Pentium Pro, Pentium II/III, Pentium 4, Xeon and AMD Athlon and Opteron processors. The total space requirement for installation (not counting the pqsv32windows.exe file which is about 6 Mbytes but can be deleted after installation) is somewhat over 20 Megabytes. Most routine jobs need very little disk space during execution. However, large MP2 energy and gradient calculations, and all and frequency calculations need a large amount of scratch disk space. The program will run best on computers with 64+ MB of memory, the more the better; the Windows output files in Gauntlet were run on an office computer with a 2.8 GHz Pentium processor and 512 MB of memory.
RUNNING THE PQS SOFTWARE
To run the program, open an MS-DOS box (from Start -> Programs ->MS-DOS, or from Run -> cmd), and INITIALIZE THE PQS ENVIRONMENT by going to the PQS directory (assumed to be C:\PQS below) and executing the batch file SETPQS.BAT (type "setpqs") at the DOS prompt (usually ">"):
>cd C:\PQS
C:\PQS>setpqs
If you installed PQS in another directory, say D:\PQS_NEW then first change to the D disk by typing D: at the prompt, then go to the PQS directory (type
cd D:\PQS_NEW) as shown below:
>D:
>cd D:\PQS_NEW
D:\PQS_NEW>setpqs
Substitute the appropriate install directory for PQS_NEW if you installed PQS in another directory.
** To run pqsv32 in unlimited mode you need a license file **
** See the license section later in this documentation **
** No licensing is needed for moderate-sized molecules and basis sets **
** (fewer than 25 atoms and 100 basis functions) **
** For large calculations, we recommend our parallel Linux version **
If you keep working in the same DOS window, you do not need to repeat this setup step. However, if you close your window by typing "exit" or by clicking on the "x" in the right-hand corner of your window, and then open a new window, you will have to type "setpqs" again.
You can now prepare an input file using a text editor (or better, you may want to construct a molecule first, using a modeling package such as PC‑MODEL, Spartan, Hyperchem, Cerius, etc.). (The next version of our Windows software will come with a built-in builder and graphical user interface. We already offer the GUI for Linux, and the builder is close to release.) The default extension of the input file is .inp, e.g., heptane.inp Detailed instructions on the PQS input file are given in the PQS Manual (pqs-man.pdf, pqs-man.txt or pqs-man.htm) in the DOC directory, and, most conveniently, in the online manual. To use the latter, double click on MANUAL.html in the ONLINE_PQS_MAN directory. If the red CONTENT panel on the left side is not visible or not wide enough, move its border by left-clicking and holding down the button. Note that ONLINE_PQS_MAN is updated less frequently than the files in the DOC directory. For instance, the current distribution still contains the 3.0 version of ONLINE_PQS_MAN, and therefore does not contain the latest additions, for instance MP2 gradients, the COSMO solvation model, or newer exchange-correlation functionals and effective core potentials, and numerous smaller improvements. If in doubt, consult pqs-man.pdf, htm or txt.
Both PQS style and Pople style inputs can be used. The examples in GAUNTLET\EXAMPLE contain both types. GAUNTLET\SMALL and GAUNTLET\MID contain mainly PQS style inputs. For Pople style inputs, see the examples in GAUNTLET\POPLE. The Pople style is simpler but less flexible than the PQS style.
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To test the installation, run the code with the sample input file test.inp provided in the main PQS install directory (usually C:\PQS). In the install directory,type at the DOS prompt (>) the following:
>setpqs
>pqs test.inp (or simply >pqs test
This run will also generate the LOCK CODE, necessary for obtaining a license file. The lock code is a long (usually 9 or 10 digit) integer, and should be sent to sales@pqs-chem.com for purchase, or entered on our Web site (www.pqs-chem.com) to get a demo license for larger systems (Software -> Download -> Register). Please indicate under Comments whether you would like to purchase the permanent version of the software or are interested in a limited-time demo version. In the former case, please contact sales@pqs-chem.com for payment options. See detailed instructions in Readme.txt in this directory.
Your lock code (a 9 or 10 digit number) should appear on the screen, and also printed in the file test.out. After obtaining you lock code (and payment for a permanent version), either through the Web or by E-mail, PQS will send you a license file, valid for the computer on which you generated the lock code. The license file, obtained from PQS, is called pqs_lic and has to be put in the PQS root directory. It consists of 2 large (9 or 10 digit) integers. If you type the license code in by hand, use Notepad and terminate the file pqs_lic with an empty line.
Please do not try to extend the validity of your demo license by changing the clock of your PC. The license checker will detect this and will permanently disable your PQS software. If this happens, you will have to reinstall PQS completely. For site license, please contact PQS (sales@pqs-chem.com).
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To run the program, go to the directory containing the input, e.g., C:\PQS\TESTS (by typing cd C:\PQS\TESTS),and type
>pqs <input_name>
or, preferably (assuming that your input has the standard extension .inp)
>pqs <molecule_name>.
If your input is called heptane.inp and is in C:\PQS\TESTS, then type
>cd C:\PQS\TESTS
C:\PQS\TESTS>pqs heptane
Substitute <molecule_name> for heptane in the above example if your input file has a different name. If your input file has an extension different from *.inp, you need to type the full input file name, e.g. pqs heptane.input. Note that in this case, some scripts may not work fully (e.g. old output, instead of being saved in <molecule_name>.old, may be overwritten.)
There are two output files: a long output called <molecule_name>.out, and a short output which should contain all final quantities of interest without the intermediate print out called <molecule name>.log; for the heptane example they will be heptane.out and heptane.log .
To remove intermediate files after a run, type >tidy <molecule name> in the directory in which you did the calculation.In the above example, type
C:\PQS\TESTS>tidy heptane
If you want to remove ALL temporary files in a directory, type
>tidy all
WARNING: removing the intermediate files of a running job will cause the job to crash.
It is advisable to remove stale files with the TIDY command, especially in geometry optimization runs, unless you want to continue an optimization. An optimization which is killed manually may leave an .optchk file which can be used for restarts. This file will interfere with your job if you want to submit it again from the beginning. If you want to keep other files (e.g. molecular orbitals), then remove the *.optchk file manually, or use the CLEAN option in the next run of the optimizer (see the manual).
CONTENTS OF THE INSTALLATION DIRECTORIES
The installation directory contains the following subdirectories:
BASDIR DOC GAUNTLET ONLINE_PQS_MAN SCR
DOC contains the manual in 3 forms: a PDF file, a text file, and a plain HTM file. ONLINE_PQS_MAN contains a very handy interactive version of the manual. However, it is currently referring to the 3.0 version only.
BASDIR contains the basis set libraries. A large number of commonly used basis sets are included.
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GAUNTLET contains test jobs, in four subdirectories:
EXAMPLES SMALL MID POPLE BIG and XL.
EXAMPLES contain small jobs intended to demonstrate the program features. SMALL and MID contain somewhat larger calculations. POPLE contains test jobs using the Pople style input. BIG contains jobs which were considered unsuitable for Windows PCs a few years ago but they pose no problems on an average office computer now. The full test suite contains also an XL (extra large) directory but this is not intended to be run with the Windows version. These large jobs are meant to test the parallel capabilities of the PQS suite on our parallel Linux workstations.
Each of the above directories except XL contains a subdirectory OUT, containing test results run on a 2.8 GHz Pentium (an ordinary office computer). If you run the jobs in the GAUNTLET suite, the results should be essentially the same as those in the OUT directories. Minor differences are possible due to round-off, or improvements in the software. The EXAMPLES, SMALL, and POPLE directories also have an OUT1-Linux subdirectory, containing single processor outputs obtained on a 2.0 GHz Opteron system under Linux.
The MID, LARGE and XL directories contain, in addition, a directory OUT4-Linux (OUT8-Linux for XL). The results in this directory have been run in parallel on 4 or 8 processors on our QuantumStation (in dual processor mode).
To run any full set of test jobs (e.g., all the jobs in the EXAMPLES directory), there is a batch file included in each directory, e.g., examples.bat in EXAMPLES, small.bat in SMALL, etc.. To run the WHOLE set of tests, type gauntlet (or gauntlet.bat) in the GAUNTLET directory. Be warned that this may take over a day (or more on an older computer).
SCR is the default PQS scratch directory. It can be cleaned by the TIDY command (see above).
LICENSE
By installing the software, the user acknowledges that he/she will observe the conditions laid down in the LICENSE AGREEMENT. When publishing results obtained using the PQS software, the user should reference PQS as described in the PQS Manual.
If you run the PQSv32 executable without a license file, you will get a message warning you that larger calculations need a license. This message also gives your lock code. If you try to run a calculation that exceeds the limits of the free version, you will get a message like this:
No valid license file <pqs_lic> found in C:\PQS
Your lock code is <9/10 digit integer>
You should send this 9 or 10 digit LOCK CODE to PQS (either by email to sales@pqs-chem.com or by registering at http://www.pqs-chem.com/software.shtml) to obtain your license code. The license code consists of two 9 or 10-digit numbers, separated by spaces. Put these numbers exactly as returned to you in the file pqs_lic in your PQS root (install) directory (default C:\PQS)., and terminate the license file by an empty line. Temporary trial licenses for Windows are issued only if there is a sufficient reason because tests for moderately sized molecules can be conducted without a license. The license for the SQM program should also be included in the same file pqs_lic (pqs_lic can have an unlimited number of license codes as long as it contains the code for the current machine). Please copy the license code directly from our E-mail, or type it using Notepad and TERMINATE THE LICENSE FILE (pqs_lic) WITH AN EMPTY LINE.
** IMPORTANT: The program generates a lock code only the first time it is**
** run without a license. This lock code is stored on the computer. Do not remove until you have installed the license file. **
** Otherwise, the program will generate a new lock code, invalidating**
**the original lock code**
Please do not try to extend the validity of your demo license by setting back the clock of your PC. In such a case, the license checker will permanently disable your version of PQS. In such a case, you will have to reinstall it completely and request a new license code.
Note that Parallel Quantum Solutions, LLC (PQS) does not offer any explicit or implicit guarantees that the software will always work, or that the results are accurate and/or appropriate to your purpose. The PQS warranty is limited to the purchase price of the software.
In case of difficulties, you may contact PQS, LLC by E-mail at tech@pqs-chem.com
Parallel Quantum Solutions,
To inquire about our PC-based parallel supercomputers, visit our Web site www.pqs-chem.com, or send E-mail to sales@pqs-chem.com.
The install program will also install the Scaled Quantum Mechanical (SQM) program in a subdirectory of PQS. SQM is a self-standing program. Although it is intended for use with the PQS software, it can also use force constants from other programs, for instance Gaussian, with appropriate conversion scripts. SQM requires a license code. This should be put in the same file (pqs_lic in the PQS install directory) as the PQS license, see the comment above. The file pqs_lic can have an unlimited number of license codes in separate lines. It is not necessary to have a PQS license for SQM to work, although most users probably will use it this way.