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  ÇöÀçÀ§Ä¡ ► ZanNavi's space : Research : G94-FREQ  

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1997-1999 @KAIST

Gaussian94ÀÇ frequency°è»ê¿¡¼­ vibrational mode¸¦ º¸´Â ¹æ¹ý


Gaussian94ÀÇ freqency °è»ê °á°ú¸¦ °¡Áö°í HyperChem¿Í Cerius2À» ÀÌ¿ëÇÏ¿© vibrational mode¸¦ º¸¿©ÁÖ´Â ¹æ¹ýÀ» ¾Ë¾Æº»´Ù.
  ¸ÕÀú G94·Î °è»êÀ» ÇÒ¶§ ¹Ýµå½Ã checkpoint ÆÄÀÏÀ» ¸¸µé¾îµÐ´Ù. HyperChemÀÇ script ÆÄÀϱ¸Á¶¸¦ Àß ¾Ë°í ÀÖ´Ù¸é G94ÀÇ log ÆÄÀϷκÎÅÍ Á¤º¸¸¦ ¾ò¾î³¾¼öµµ ÀÖÁö¸¸ checkpoint ÆÄÀÏÀ» ¸¸µé¾îµÎ´Â °ÍÀÌ ¿©·¯¸ð·Î Æí¸®ÇÏ´Ù.

  1. HyperChemÀ» ÀÌ¿ëÇÏ´Â ¹æ¹ý
    freqchk¶ó´Â Gaussian À¯Æ¿¸®Æ¼¸¦ ÀÌ¿ëÇÑ´Ù. »ç¿ë¹ýÀº ¸Å¿ì °£´ÜÇÏ¿©
              freqchk ¶Ç´Â
              freqchk [chk file]
    
    ÇÏ¸é µÈ´Ù. ¸í·ÉÇà¿¡¼­ ÆÄÀÏÀ̸§À» ÁöÁ¤ÇØÁÖÁö ¾ÊÀ¸¸é checkpoint ÆÄÀÏÀ̸§À» ¹°¾îº¸°Ô µÈ´Ù. ±× ´ÙÀ½Àº
              Write Hyperchem files? 
    
    °£´ÜÈ÷ y¶ó°í ÃÄÁÖ¸é µÈ´Ù. Á¤¸» ½±Áö ¾ÊÀº°¡?
      ´ÙÀ½ Áú¹®Àº isotope mass¸¦ ¹°¾îº»´Ù. y¶ó°í ÃÄÁÖ¸é principal isotope mass¸¦ ¾Ë¾Æ¼­ ³Ö¾îÁÖ°Ô µÇ°í nÀ¸·Î ´äÇÏ¸é °¢ atom¸¶´Ù isotope mass¸¦ ¹°¾îº»´Ù. ±ÙóÀÇ Á¤¼ö°ªÀ» ³Ö¾îÁÖ¸é ¾Ë·ÁÁ®ÀÖ´Â isotope mass°ª Áß Çϳª¸¦ ÅÃÇÏ¿© Á¤È®ÇÑ °ªÀ» ÀÔ·ÂÇØÁØ´Ù. ÇÑ°¡Áö ¾Æ½¬¿î °ÍÀº isotope mass°ªÀ» ÀÓÀÇ·Î Á¤ÇØÁÙ¼ö ¾ø´Ù.
      ÀÔ·ÂÀÌ ³¡³µÀ¸¸é °°Àº µð·ºÅ丮¿¡ freqchk.ent¿Í freqchk.scrÀÌ »ý±ä´Ù. ¾ÕÀÇ °ÍÀº ºÐÀÚÀÇ geometry¸¦ ´ã°íÀÖ´Â PDBÆÄÀÏÀÌ°í, µÚÀÇ °ÍÀº HyperChem¿¡¼­ »ç¿ëÇÏ´Â scriptÆÄÀÏÀÌ´Ù.
      HyperChemÀ» ½ÇÇàÇÑÈÄ Script¸Þ´º¿¡¼­ freqchk.scrÀ» openÇÏ¸é ¾Ë¾Æ¼­ PDBÆÄÀÏÀ» ºÒ·¯¿À°í ¾î¶² vibrational mode¸¦ ¼±ÅÃÇÒ °ÍÀÎÁö ¹°¾îº¸¸ç, ¼±ÅÃÇÑ mode¸¦ µ¿¿µ»óÀ¸·Î º¸¿©ÁØ´Ù. ´Ù¸¥ mode¸¦ ¼±ÅÃÇÏ·Á¸é Cancel¸Þ´º·Î script¸¦ ¸ØÃá ´ÙÀ½, Compute¸Þ´º¿¡ Vibrational Spectrum...À» ¼±ÅÃÇÑ´Ù.
      freqchk´Â Ç×»ó freqchk.ent¿Í freqchk.scr¶ó´Â À̸§ÀÇ ÆÄÀϸ¸À» ¸¸µç´Ù. ÀÌ À̸§À» ¹Ù²Ù·Á¸é freqchk.scrÆÄÀÏÀÇ µÎ¹ø° ÁÙÀ» ¹Ù²Ü À̸§À¸·Î °íÃÄÁÖ¾î¾ß ÇÑ´Ù. ÀÌ·¯ÇÑ ÀÛ¾÷Àº ´ÙÀ½°ú °°Àº freq2hyper¶õ shell script¸¦ ¸¸µé¾î¼­ »ç¿ëÇϸé Æí¸®ÇÏ´Ù.
    freq2hyper
    ---------------------------------------------------------------------------
    #!/usr/local/bin/bash
    
    function error() {
      echo -e "$1"
      exit
    }
    
    # ¾Æ¹« ÀÎÀÚ°¡ ÁÖ¾îÁöÁö ¾ÊÀ¸¸é »ç¿ë¹æ¹ýÀ» Ãâ·ÂÇÏ°í ³¡³¿
    [ $1 ] || error "USAGE : freq2hyper chk_file[.chk]";
    
    FILE_ROOT="${1%.chk}"
    CHK=$FILE_ROOT.chk
    
    # ¸í·ÉÇà ÀÎÀÚ·Î ÁÖ¾îÁø chkÆÄÀÏÀÌ ÀÖ´ÂÁö °Ë»ç
    [ -f $CHK ] || error "$CHK ÆÄÀÏÀÌ ¾ø½À´Ï´Ù.";
    
    # chkchk : checkpoint ÆÄÀÏ¿¡ ´ëÇÑ Á¤º¸¸¦ ¾Ë·ÁÁÖ´Â Gaussian À¯Æ¿¸®Æ¼
    # freq¿¡ ´ëÇÑ Á¤º¸°¡ ÀÖ´ÂÁö °Ë»çÇÑ´Ù.
    (chkchk $CHK | grep "Cartesian force constants present." > /dev/null) \
      || error "$CHK ÆÄÀÏ¿¡ cartesian force constant¿¡ ´ëÇÑ Á¤º¸°¡ ¾ø½À´Ï´Ù.\nfrequency °è»êÀÌ ¸Â´ÂÁö È®ÀÎÇØ ÁֽʽÿÀ.";
    
    # freqchk : frequencyÁ¤º¸¸¦ »Ì¾Æ³»´Â Gaussian À¯Æ¿¸®Æ¼
    # HyperChemÇü½ÄÀ¸·Î Ãâ·Â
    echo " ----------------------------------------------------------"
    echo -e "y\ny" | freqchk $CHK | tail +2
    
    # »ý¼ºµÈ freqchk.* ÆÄÀÏÀ» ÁÖ¾îÁø À̸§À¸·Î º¯°æ
    mv freqchk.ent $FILE_ROOT.ent
    sed "s/freqchk.ent/$FILE_ROOT.ent/" freqchk.scr > $FILE_ROOT.scr
    rm -f freqchk.scr
    ---------------------------------------------------------------------------
    
    
  2. Cerius2À» ÀÌ¿ëÇÏ´Â ¹æ¹ý
    formchk¶ó´Â Gaussian À¯Æ¿¸®Æ¼¸¦ ÀÌ¿ëÇÑ´Ù.
              formchk ¶Ç´Â
              formchk [chk file]
    
    ¶ó°í Çϸé .fchk ÆÄÀÏÀÌ »ý¼ºµÇ¸ç ÀÌ ÆÄÀÏÀ» Cerius2¿¡¼­ Á÷Á¢ ÀÐÀ»¼ö ÀÖ´Ù. fchk ÆÄÀÏÀº textÇü½ÄÀ̹ǷΠ³»¿ëÀ» º¼¼öµµ ÀÖÀ¸¸ç ´Ù¸¥ ±âÁ¾ÀÇ ÄÄÇ»ÅÍ·Î °¡Á®°¡±âµµ ½±´Ù.
      Cerius2ÀÇ Gaussian module¿¡¼­ AnalyzeÀÇ File¸Þ´º¿¡¼­ fchk ÆÄÀÏÀ» ÀÐÀº ´ÙÀ½, Vibrations¸Þ´º¿¡¼­ Calculate Vibrational Normal Modes¸¦ ´©¸£¸é °¢ mode°¡ °è»êµÇ¸é¼­ ¼±ÅÃÀ» ÇÒ¼ö ÀÖ°Ô µÇ°í ANIMATE¸¦ ´©¸£¸é µ¿¿µ»óÀ¸·Î º¸¿©ÁØ´Ù. translation°ú rotationµµ °°ÀÌ Æ÷ÇԵȴٴ Á¡ÀÌ HyperChem°ú ´Ù¸¥ Á¡ÀÌ´Ù.
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