[Patch] Unpaired_electron_population (Molds-dev) - MolDS

Dear Okuyama,

Thanks for your patches. I had reviewed them.

***
Your coding-grammar and -style are quite fine!
But, I ask you to fix only one modification about input control:
(1) UEP should be set as "unpaired_electron_population yes" in CIS-directive,
    that is, the following input obeys the MolDS's input style.

    CIS
      ....
      mulliken m
      mulliken n
      unpaired_electron_population yes
      ....
    END

    The corresponding code in the InputParser.cpp (r1234 which your 2
patches and my modification had been applied to) is written as

    742 int InputParser::ParseConditionsCIS(vector<string>*
inputTerms, int parseIndex) const{
    743    Parameters::GetInstance()->SetRequiresCIS(true);
    744    parseIndex++;
     .
     .
     .
     .
    827       // unpaired electron population
    828       if((*inputTerms)[parseIndex].compare(this->stringCISUnpairedPop)
== 0){
    829          if((*inputTerms)[parseIndex+1].compare(this->stringYES) == 0){
    830             Parameters::GetInstance()->SetRequiresUnpairedPopCIS(true);
    831          }
    832          else{
    833             Parameters::GetInstance()->SetRequiresUnpairedPopCIS(false);
    834          }
    835          parseIndex++;
    836       }
    837       parseIndex++;
    838    }
    839    return parseIndex;
    840 }

With integration of the (1) to your second patch "add_opt_ctrl.patch",
please commit your code to the trunk.

***
Besides, I ask you to do two more tasks about this ticket.
[1] Update test input and output files in the molds/trunk/test for the UEP.
    I think that updating of only "c2h6_pm3_directCIS_singlet.in" and
"c2h6_pm3_directCIS_singlet.dat" is enough.
[2] Update documents (molds/trunk/doc/README.txt) to use UEP.
    Explanation of the UEP option should be written in the
<CIS>-paragraph of the README.txt.

Of course, please commit [1] and [2] too.

Please ask me if you have any question.
My best,
Mikiya

***************************************
Mikiya Fujii, Ph.D.

Yamashita & Ushiyama Laboratory,
Department of Chemical System Engineering,
Faculty of Engineering,
The University of Tokyo.

tel&fax: +81-3-5841-7286
email: fujii****@tcl*****
HP: http://www.tcl.t.u-tokyo.ac.jp/
***************************************

2013/1/4 Okuyama <okymm****@gmail*****>:
> Dear colleagues
>
> This is Okuyama.
>
> I send patch files to impliment the unpaired electron population (UEP)
> and the input control to this mailing list.
> The patch files are the following files:
>      *calc_uep_without_opt_ctrl.patch
>      *add_opt_ctrl.patch
>
> calc_uep_without_opt_ctrl.patch adds source code to be available the
> unpaired electron population.
> By appling this patch file, it's possible to calculate the unpaired
> electron population of excited states on each single atom in molecule.
> Upto this implimentation, you can calculate the unpaired electron
> population of nth-excited states
> by adding the follwing input:
>      CIS
>          mulliken n
>      END
> Next, the file, add_opt_ctrl.patch adds the input control of the
> unpaired electron population.
> The input control executes the calculation of the UEP
> when there is a keyword, 'unpaired_electron_population' in the CIS input.
>
> *Procedure to apply the patch files to the MolDS
>      Revision of the Molds is 1234
>      In a directory, trunk,
>      1. patch -p0 < calc_uep_without_opt_ctrl.patch
>      2. patch -p2 < add_opt_ctrl.patch
>
> *How to use the UEP calculation
> Example) Calculation of the UEP of the m and n-th excited states
> CIS
>      ....
>      mulliken m
>      mulliken n
>      unpaired_electron_population
>      ....
> END
>
> I have made sure the following terms:
>      * There are not segmentation fault and abort by executing all the
> test inputs.
>      * The MolDS.out is created by executing make depend INTEL=64 &&
> make INTEL=64
>      * For all the test inputs including CIS keyword, I added the
> follwing keyword:
>          CIS
>              ....
>              mulliken 2
>              mulliken 3
>              unpaired_electron_population
>              ...
>          END
>        Under above condition, I make sure that there is no segmentation
> fault.
>
> At last, in this implimentation, it will not calculate the UEP at the
> ground state.
> The reason why the UEP at the ground state is zero and, therefore this
> calculation is nonsense.
>
> Best regards.
>
> -------------- next part --------------
> テキスト形式以外の添付ファイルを保管しました...
> ファイル名: calc_uep_without_opt_ctrl.patch
> 型:         text/x-patch
> サイズ:     8604 バイト
> 説明:       無し
> Download
> -------------- next part --------------
> テキスト形式以外の添付ファイルを保管しました...
> ファイル名: add_opt_ctrl.patch
> 型:         text/x-patch
> サイズ:     4357 バイト
> 説明:       無し
> URL:        http://lists.sourceforge.jp/mailman/archives/molds-dev/attachments/20130104/ce956b15/attachment-0001.bin
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[Molds-dev] [Patch] Unpaired_electron_population