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Home modified by

Wed, 10 Apr 2013 09:36:48 -0000

--- v20
+++ v21
@@ -1,40 +1,37 @@
-*mobcalPARSER*
+mobcalPARSER
 ==================
-Purpose
-------------------
-The program is intended to provide an easy to use Windows/Linux portable interface between ab initio program output (support for Gaussian 94/98/03/09, Orca 2.7/2.8, Jaguar and NWchem) and Prof. M.F. Jarrold's MOBCAL program. Additionally, different molecular structure file formats are supported (*.mol, *.xyz, *.pdb), such that force field and molecular dynamics data can also be used (e.g. Tinker). The user can choose whether or not he/she wishes the program to act interactively (see full release notes).
+is intended to provide an easy to use Windows/Linux portable interface between ab initio program output (support for Gaussian 94/98/03/09, Orca 2.7/2.8, Jaguar and NWchem) and Prof. M.F. Jarrold's MOBCAL program. Additionally, different molecular structure file formats are supported (*.mol, *.xyz, *.pdb), such that force field and molecular dynamics data can also be used (e.g. Tinker). The user can choose whether or not he/she wishes the program to act interactively (see full release notes).

-Configuration
-------------------
-*MOBCAL is available at , the source is NOT provided here.*
- 
-* When you're working under Win32 you can use Force 2.0.9 to compile mobcal.exe from mobcal.f. Alternatively you can use gfortran from the MinGW package.
-* Under Linux you can use gfortran, set the legacy flag (-std=legacy) to compile fortran77 code and make the compiled file executable (chmod +x ...).
+#### Configuration ####
+MOBCAL is available from Prof. M. F. Jarrold's webpage, *the source is NOT provided here.*
+####  ####
+When you're working under Win32 you can use Force 2.0.9 to compile mobcal.exe from mobcal.f. Alternatively you can use gfortran from the MinGW package. Under Linux you can use gfortran, set the legacy flag (-std=legacy) to compile fortran77 code and make the compiled file executable (chmod +x ...). g77 can also be used. 

-Once you have compiled a working MOBCAL executable, simply place mobcalPARSER.pl in the same directory. Under Win32 you need to install a PERL runtime environment, if you're new to PERL go to: . You will not need any additional PERL packages to run mobcalPARSER with basic functionality. ActivePERL was used to develop the program, but StrawberryPERL works as well.
+* 
+* 

-mobcalPARSER is preconfigured for Win32 environment, under Linux you need to start mobcalPARSER.pl once to generate a fresh config.cfg. In the new config.cfg, replace the line that reads "mobcal.exe" (found in line 7/8) by something like "mobcal", where mobcal is the filename of the compiled mobcal.f (no quotation marks!). Most Linux distributions already contain PERL, but you might want to change the first line in mobcalPARSER.pl from: #usr/bin/perl to #"YOUR_PERL_PATH".
+Once you have compiled a working MOBCAL executable, simply place mobcalPARSER.pl in the same directory. Under Win32 you need to install a PERL runtime environment. You will not need any additional PERL packages to run mobcalPARSER with basic functionality. ActivePERL was used to develop the program, but StrawberryPERL works as well.

-Under Linux you might want to enable colored ANSI screen output, go to config.cfg and change the default value "NO" in line 5/8 to "yes". You'll get a better readable screen output.
+* . 
+* 
+* 

-Testing
-------------------
-You might want to consider downloading avogadro at . Load C60 fullerene geometry from fragments, save it as xyz, mol or pdb file and place in the same directory as mobcalPARSER.pl and MOBCAL executable. Run the script and wait until MOBCAL is finished.
+mobcalPARSER is preconfigured for Win32 environment, under Linux you need to start mobcalPARSER.pl once to generate a fresh config.cfg. In the new config.cfg, replace the line that reads "mobcal.exe" (found in line 7/8) by something like "mobcal", where mobcal is the filename of the compiled mobcal.f (no quotation marks!). Most Linux distributions already contain PERL, but you might want to change the first line in mobcalPARSER.pl from: #usr/bin/perl to #"YOUR_PERL_PATH". Under Linux you might want to enable colored ANSI screen output, go to config.cfg and change the default value "NO" in line 5/8 to "yes". You'll get a better readable screen output.

-Full release notes
-------------------
-Please type mobcalPARSER.pl h to view the release notes and additional features.
+#### Full release notes & testing ####
+Please type mobcalPARSER.pl h to view the release notes and additional features. You might want to consider downloading avogadro at 

-License
-------------------
-As is customary, this program is licensed under the terms of the artistic license. http://en.wikipedia.org/wiki/Artistic_License
+* .

-Citation
-------------------
-The *Artistic License* does not require you to cite this software, i.e. this interface is not "cite-ware", *but all the programs that are interfaced are*. Relevant citations are found in the log file (v0.0.8).
+Load C60 fullerene geometry from fragments, save it as xyz, mol or pdb file and place in the same directory as mobcalPARSER.pl and MOBCAL executable. Run the script and wait until MOBCAL is finished.
+
+#### License & Citation ####
+As is customary, this program is licensed under the terms of the *Artistic License*. 
+
+* 
+
+The *Artistic License* does not require you to cite this software, *i.e. this interface is not citeware, but all programs that are interfaced are.* Relevant citations are found in the log file (v0.0.8).

 * Windows (v0.0.8): c switch opens a set of relevant links in the browser. 

-If you use mobcalPARSER in a scientific publication or thesis, you may include the following line in your references section, but you are not obliged to: mobcalPARSER, ver. X.Y.Z (http://sourceforge.net/projects/mobcalparser/).
-
 lycæum@web.de, 8-4-2013

Home modified by

Mon, 08 Apr 2013 23:17:40 -0000

--- v19
+++ v20
@@ -35,6 +35,6 @@

 * Windows (v0.0.8): c switch opens a set of relevant links in the browser. 

-If you use mobcalPARSER in a scientific publication or thesis, you *can* include the following line in your references section, but you are not obliged to: mobcalPARSER, ver. X.Y.Z (http://sourceforge.net/projects/mobcalparser/).
+If you use mobcalPARSER in a scientific publication or thesis, you may include the following line in your references section, but you are not obliged to: mobcalPARSER, ver. X.Y.Z (http://sourceforge.net/projects/mobcalparser/).

 lycæum@web.de, 8-4-2013

Home modified by

Mon, 08 Apr 2013 19:26:09 -0000

--- v18
+++ v19
@@ -31,11 +31,10 @@

 Citation
 ------------------
-The *Artistic License* does not require you to cite this software, i.e. this interface is not "cite-ware", *but all the programs that are interface are*. Relevant citations are found in the log file (v0.0.8).
+The *Artistic License* does not require you to cite this software, i.e. this interface is not "cite-ware", *but all the programs that are interfaced are*. Relevant citations are found in the log file (v0.0.8).

 * Windows (v0.0.8): c switch opens a set of relevant links in the browser. 

-If you use mobcalPARSER in a scientific publication or thesis, you *can* include the following line in your references section, but you are not obliged to.
-mobcalPARSER, ver. X.Y.Z (http://sourceforge.net/projects/mobcalparser/).
+If you use mobcalPARSER in a scientific publication or thesis, you *can* include the following line in your references section, but you are not obliged to: mobcalPARSER, ver. X.Y.Z (http://sourceforge.net/projects/mobcalparser/).

 lycæum@web.de, 8-4-2013

Home modified by

Mon, 08 Apr 2013 19:24:04 -0000

--- v17
+++ v18
@@ -27,7 +27,7 @@

 License
 ------------------
-This program is licensed under the terms of the artistic license. http://en.wikipedia.org/wiki/Artistic_License
+As is customary, this program is licensed under the terms of the artistic license. http://en.wikipedia.org/wiki/Artistic_License

 Citation
 ------------------

Home modified by

Mon, 08 Apr 2013 19:19:50 -0000

--- v16
+++ v17
@@ -1,10 +1,10 @@
-Getting started
+*mobcalPARSER*
 ==================
-What dœs mobcalPARSER do?
+Purpose
 ------------------
 The program is intended to provide an easy to use Windows/Linux portable interface between ab initio program output (support for Gaussian 94/98/03/09, Orca 2.7/2.8, Jaguar and NWchem) and Prof. M.F. Jarrold's MOBCAL program. Additionally, different molecular structure file formats are supported (*.mol, *.xyz, *.pdb), such that force field and molecular dynamics data can also be used (e.g. Tinker). The user can choose whether or not he/she wishes the program to act interactively (see full release notes).

-Obtaining and Compiling MOBCAL, Configuring mobcalPARSER
+Configuration
 ------------------
 *MOBCAL is available at , the source is NOT provided here.*

@@ -17,7 +17,7 @@

 Under Linux you might want to enable colored ANSI screen output, go to config.cfg and change the default value "NO" in line 5/8 to "yes". You'll get a better readable screen output.

-Obtaining structures to test your setup
+Testing
 ------------------
 You might want to consider downloading avogadro at . Load C60 fullerene geometry from fragments, save it as xyz, mol or pdb file and place in the same directory as mobcalPARSER.pl and MOBCAL executable. Run the script and wait until MOBCAL is finished.

@@ -25,9 +25,17 @@
 ------------------
 Please type mobcalPARSER.pl h to view the release notes and additional features.

-How to cite mobcalPARSER
+License
 ------------------
-If you use mobcalPARSER in a scientific publication or thesis, you can include the following line in your references section, replace "X.Y.Z" by the version you used.
+This program is licensed under the terms of the artistic license. http://en.wikipedia.org/wiki/Artistic_License
+
+Citation
+------------------
+The *Artistic License* does not require you to cite this software, i.e. this interface is not "cite-ware", *but all the programs that are interface are*. Relevant citations are found in the log file (v0.0.8).
+
+* Windows (v0.0.8): c switch opens a set of relevant links in the browser. 
+
+If you use mobcalPARSER in a scientific publication or thesis, you *can* include the following line in your references section, but you are not obliged to.
 mobcalPARSER, ver. X.Y.Z (http://sourceforge.net/projects/mobcalparser/).

-lycæum@web.de, 3-31-2013
+lycæum@web.de, 8-4-2013

Home modified by

Thu, 04 Apr 2013 00:35:52 -0000

--- v15
+++ v16
@@ -19,7 +19,7 @@

 Obtaining structures to test your setup
 ------------------
-You might want to consider downloading avogadro . Load C60 fullerene geometry from fragments, save it as xyz, mol or pdb file and place in the same directory as mobcalPARSER.pl and MOBCAL executable. Run the script and wait until MOBCAL is finished.
+You might want to consider downloading avogadro at . Load C60 fullerene geometry from fragments, save it as xyz, mol or pdb file and place in the same directory as mobcalPARSER.pl and MOBCAL executable. Run the script and wait until MOBCAL is finished.

 Full release notes
 ------------------

Home modified by

Thu, 04 Apr 2013 00:34:36 -0000

--- v14
+++ v15
@@ -27,7 +27,7 @@

 How to cite mobcalPARSER
 ------------------
-If you use mobcalPARSER in a scientific publication or thesis, you can include the following line in your references section, replace "X" by the version you used.
-mobcalPARSER, ver. "X.Y.Z" (http://sourceforge.net/projects/mobcalparser/).
+If you use mobcalPARSER in a scientific publication or thesis, you can include the following line in your references section, replace "X.Y.Z" by the version you used.
+mobcalPARSER, ver. X.Y.Z (http://sourceforge.net/projects/mobcalparser/).

 lycæum@web.de, 3-31-2013

Home modified by

Thu, 04 Apr 2013 00:34:03 -0000

--- v13
+++ v14
@@ -2,7 +2,7 @@
 ==================
 What dœs mobcalPARSER do?
 ------------------
-The program is intended to provide an easy to use Windows/Linux portable interface between ab initio program output (support for Gaussian 94/98/03/09, Orca 2.7/2.8, Jaguar and NWchem) and Prof. M.F. Jarrold's MOBCAL program. Additionally, different molecular structure file formats are supported (*.mol, *.xyz, *.pdb), such that force field and molecular dynamics data can also be used (e.g. Tinker). The user can choose whether or not he/she wishes "mobcalPARSER" to act interactively (see full release notes).
+The program is intended to provide an easy to use Windows/Linux portable interface between ab initio program output (support for Gaussian 94/98/03/09, Orca 2.7/2.8, Jaguar and NWchem) and Prof. M.F. Jarrold's MOBCAL program. Additionally, different molecular structure file formats are supported (*.mol, *.xyz, *.pdb), such that force field and molecular dynamics data can also be used (e.g. Tinker). The user can choose whether or not he/she wishes the program to act interactively (see full release notes).

 Obtaining and Compiling MOBCAL, Configuring mobcalPARSER
 ------------------
@@ -23,17 +23,11 @@

 Full release notes
 ------------------
-Please type mobcalPARSER_xxx.pl h to view the release notes and additional features.
-
-Why are GAMESS, ADF and TURBOMOLE not supported?
-------------------
-I do not use these programs. If you can supply me with authentic output files (e.g. C60 cation geometry optimization or protonated DMSO dimer), I can start to implement support for these program output formats. The output needs to contain some kind of charge analysis data (e.g. Mulliken, Loewdin and (or nbo).
+Please type mobcalPARSER.pl h to view the release notes and additional features.

 How to cite mobcalPARSER
 ------------------
-If you use mobcalPARSER in a scientific publication or thesis, you can include the following line in your references section:
-mobcalPARSER, ver. "X" (http://sourceforge.net/projects/mobcalparser/).
-Replace "X" by the version you used.
+If you use mobcalPARSER in a scientific publication or thesis, you can include the following line in your references section, replace "X" by the version you used.
+mobcalPARSER, ver. "X.Y.Z" (http://sourceforge.net/projects/mobcalparser/).

 lycæum@web.de, 3-31-2013
-------------------

WikiPage Home modified by

Sun, 31 Mar 2013 15:48:21 -0000

--- v12
+++ v13
@@ -1,6 +1,6 @@
 Getting started
 ==================
-What does mobcalPARSER do?
+What dœs mobcalPARSER do?
 ------------------
 The program is intended to provide an easy to use Windows/Linux portable interface between ab initio program output (support for Gaussian 94/98/03/09, Orca 2.7/2.8, Jaguar and NWchem) and Prof. M.F. Jarrold's MOBCAL program. Additionally, different molecular structure file formats are supported (*.mol, *.xyz, *.pdb), such that force field and molecular dynamics data can also be used (e.g. Tinker). The user can choose whether or not he/she wishes "mobcalPARSER" to act interactively (see full release notes).

@@ -11,7 +11,7 @@
 * When you're working under Win32 you can use Force 2.0.9 to compile mobcal.exe from mobcal.f. Alternatively you can use gfortran from the MinGW package.
 * Under Linux you can use gfortran, set the legacy flag (-std=legacy) to compile fortran77 code and make the compiled file executable (chmod +x ...).

-Once you have compiled a working MOBCAL executable, simply place mobcalPARSER.pl in the same directory. Under Win32 you need to install a PERL runtime environment, if you're new to PERL go to: . You will not need any additional PERL packages to run mobcalPARSER. ActivePERL was used to develop the program, but StrawberryPERL works as well.
+Once you have compiled a working MOBCAL executable, simply place mobcalPARSER.pl in the same directory. Under Win32 you need to install a PERL runtime environment, if you're new to PERL go to: . You will not need any additional PERL packages to run mobcalPARSER with basic functionality. ActivePERL was used to develop the program, but StrawberryPERL works as well.

 mobcalPARSER is preconfigured for Win32 environment, under Linux you need to start mobcalPARSER.pl once to generate a fresh config.cfg. In the new config.cfg, replace the line that reads "mobcal.exe" (found in line 7/8) by something like "mobcal", where mobcal is the filename of the compiled mobcal.f (no quotation marks!). Most Linux distributions already contain PERL, but you might want to change the first line in mobcalPARSER.pl from: #usr/bin/perl to #"YOUR_PERL_PATH".

@@ -25,16 +25,15 @@
 ------------------
 Please type mobcalPARSER_xxx.pl h to view the release notes and additional features.

-Issues with "mobcalPARSER"
-------------------
-If you have any Problems, please join ResearchGate and start a discusstion at {http://www.researchgate.net/topic/TWIM-MS_travelling_wave_ion_mobility_mass_spectrometry/}!
-
 Why are GAMESS, ADF and TURBOMOLE not supported?
 ------------------
-I do not use these programs. If you can supply me with authentic output files (e.g. C60 cation geometry optimization or protonated DMSO dimer), I can start to implement support for these program output formats. The output needs to contain some kind of charge analysis data (e.g. Mulliken, Loewdin and(or nbo).
+I do not use these programs. If you can supply me with authentic output files (e.g. C60 cation geometry optimization or protonated DMSO dimer), I can start to implement support for these program output formats. The output needs to contain some kind of charge analysis data (e.g. Mulliken, Loewdin and (or nbo).

 How to cite mobcalPARSER
 ------------------
 If you use mobcalPARSER in a scientific publication or thesis, you can include the following line in your references section:
 mobcalPARSER, ver. "X" (http://sourceforge.net/projects/mobcalparser/).
 Replace "X" by the version you used.
+
+lycæum@web.de, 3-31-2013
+------------------

WikiPage Home modified by

Mon, 01 Oct 2012 16:10:00 -0000

--- v11
+++ v12
@@ -2,14 +2,14 @@
 ==================
 What does mobcalPARSER do?
 ------------------
-The program is intended to provide an easy to use Windows/Linux portable interface between ab initio program output (support for Gaussian 94/98/03/09, Orca 2.7/2.8, Jaguar an NWchem) and Prof. M.F. Jarrold's MOBCAL program. Additionally, different molecular structure file formats are supported (*.mol, *.xyz, *.pdb), such that force field and molecular dynamics data can also be used. The user can choose whether or not he/she wishes "mobcalPARSER" to act interactively (see full release notes).
+The program is intended to provide an easy to use Windows/Linux portable interface between ab initio program output (support for Gaussian 94/98/03/09, Orca 2.7/2.8, Jaguar and NWchem) and Prof. M.F. Jarrold's MOBCAL program. Additionally, different molecular structure file formats are supported (*.mol, *.xyz, *.pdb), such that force field and molecular dynamics data can also be used (e.g. Tinker). The user can choose whether or not he/she wishes "mobcalPARSER" to act interactively (see full release notes).
 
 Obtaining and Compiling MOBCAL, Configuring mobcalPARSER
 ------------------
 *MOBCAL is available at , the source is NOT provided here.*
  
-* When you're working under Win32 you can use Force 2.0.9 to compile mobcal.exe from mobcal.f.
-* Under Linux you need gfortran, set the legacy flag (-std=legacy) to compile fortran77 code and make the compiled file executable (chmod +x ...).
+* When you're working under Win32 you can use Force 2.0.9 to compile mobcal.exe from mobcal.f. Alternatively you can use gfortran from the MinGW package.
+* Under Linux you can use gfortran, set the legacy flag (-std=legacy) to compile fortran77 code and make the compiled file executable (chmod +x ...).
 
 Once you have compiled a working MOBCAL executable, simply place mobcalPARSER.pl in the same directory. Under Win32 you need to install a PERL runtime environment, if you're new to PERL go to: . You will not need any additional PERL packages to run mobcalPARSER. ActivePERL was used to develop the program, but StrawberryPERL works as well.