{"id":552,"date":"2022-11-18T12:11:40","date_gmt":"2022-11-18T04:11:40","guid":{"rendered":"https:\/\/www.homechemer.com\/?p=552"},"modified":"2023-06-12T18:55:33","modified_gmt":"2023-06-12T10:55:33","slug":"%e5%88%86%e5%ad%90%e8%bd%a8%e9%81%93%e5%a4%84%e7%90%86%e6%87%92%e4%ba%ba%e8%84%9a%e6%9c%ac","status":"publish","type":"post","link":"https:\/\/www.homechemer.com\/computchem\/6","title":{"rendered":"\u5206\u5b50\u8f68\u9053\u5904\u7406\u61d2\u4eba\u811a\u672c"},"content":{"rendered":"\n

\u5206\u5b50\u8f68\u9053\u5904\u7406\u61d2\u4eba\u811a\u672c
One-Key Research Scripts for Molecular Orbitals<\/strong><\/p>\n\n\n\n

Jiawei Xu
Released: 2022-11-18 \/ Updated: 2022-11-18<\/p>\n\n\n\n

\u5f53\u6709\u5927\u91cf\u5206\u5b50\u8f68\u9053\u6570\u636e\u9700\u8981\u5904\u7406\u548c\u4f5c\u56fe\u65f6\uff0c\u61d2\u4eba\u811a\u672c\u662f\u5341\u5206\u5b9e\u7528\u7684\u3002\u7c7b\u4f3c\u7684\u505a\u6cd5\u4e5f\u53ef\u4ee5\u7528\u4e8e\u5904\u7406\u5176\u4ed6\u683c\u70b9\u6570\u636e\u7684\u4f5c\u56fe\u3002<\/p>\n\n\n\n

1. \u63d0\u53d6\u5206\u5b50\u8f68\u9053\u80fd\u91cf<\/strong><\/p>\n\n\n\n

\u4f7f\u7528\u65b9\u6cd5\uff1apython OrbEne.py Gaussian16.log [orblist.txt] [orbene.txt]
\u7a0b\u5e8f\u9ed8\u8ba4\u4ece\u5f53\u524d\u76ee\u5f55\u4e0b\u7684orblist.txt\u83b7\u53d6\u9700\u8981\u8f93\u51fa\u80fd\u91cf\u7684\u5206\u5b50\u8f68\u9053\u5e8f\u53f7\uff0c\u4eceGaussian16.log\u83b7\u53d6\u7ed3\u679c\u8f93\u51fa\u5230orbene.txt\u3002orblist.txt\u7684\u8bed\u6cd5\u683c\u5f0f\u793a\u4f8b\uff1a<\/p>\n\n\n\n

15 18 to 24 30 to 28 # Get MOs numbered with 15, 18-24 and 28-30.\nh to h-5 l+1 # HOMO-5 to HOMO and LUMO+1\na h-3 to l+3 # Alpha-MOs from HOMO-3 to LUMO+3<\/code><\/pre>\n\n\n\n
\u7a0b\u5e8f\u4f1a\u81ea\u52a8\u8bc6\u522b\u662f\u5426\u4e3a\u5f00\u58f3\u5c42\u4f53\u7cfb\u3002\u53ef\u5728orblist.txt\u4e2d\u5199\u5165\u591a\u884c\uff0c\u7a0b\u5e8f\u4f1a\u5168\u90e8\u8bfb\u53d6\u3001\u6574\u7406\u6392\u5e8f\u540e\u8f93\u51fa\uff0c\u5e76\u540c\u65f6\u8f93\u51faHOMO-LUMO gap\u4fe1\u606f\u3002<\/p>\n\n\n\n
import sys\r\n\r\ndef is_number(s):\r\n    try:\r\n        float(s)\r\n        return True\r\n    except ValueError:\r\n        pass\r\n    try:\r\n        import unicodedata\r\n        unicodedata.numeric(s)\r\n        return True\r\n    except (TypeError, ValueError):\r\n        pass\r\n    return False\r\n\r\ndef orb_ene(output,spin=0):\r\n    flag=False\r\n    occ,vir=[],[]\r\n    ab=['Alpha','Beta']\r\n    with open(output,'r') as read:\r\n        for line in read.readlines():\r\n            l=line.split()\r\n            if len(l)>4:\r\n                if l[0]=='The' and l[1]=='electronic' and l[2]=='state':\r\n                    flag=True\r\n                    occ,vir=[],[]\r\n                    continue\r\n                if flag and l[0]==ab[spin] and l[1]=='occ.' and l[2]=='eigenvalues':\r\n                    for i in range(len(l)-4):\r\n                        occ.append(l[4+i])\r\n                    continue\r\n                elif flag and l[0]==ab[spin] and l[1]=='virt.' and l[2]=='eigenvalues':\r\n                    for i in range(len(l)-4):\r\n                        vir.append(l[4+i])\r\n                    continue\r\n                if l[0]=='Condensed' and l[1]=='to' and l[2]=='atoms':\r\n                    flag=False\r\n    return occ,vir\r\n\r\ndef parse(occ,src):\r\n    res=0\r\n    mo1=['h','l']\r\n    mo2=['-','+']\r\n    for i in range(2):\r\n        if is_number(src):\r\n            res=int(src)\r\n        elif src[0]==mo1[i]:\r\n            if src==mo1[i]:\r\n                res=len(occ)+i\r\n            elif len(src)>2 and src[1]==mo2[i]:\r\n                dis=int(src[2:])\r\n                res=len(occ)+dis*(2*i-1)+i\r\n    return res\r\n\r\ndef relist(occ,listfile):\r\n    orblist=[[],[]]\r\n    tmp1,tmp2=0,0\r\n    spin=0\r\n    with open(listfile,'r') as read:\r\n        for line in read.readlines():\r\n            l=line.split()\r\n            if l[0]!='b':\r\n                pass\r\n            else:\r\n                spin=1\r\n            if len(l)!=0:                \r\n                for i in range(len(l)):\r\n                    if is_number(l[i]) or l[i][0]=='h' or l[i][0]=='l':\r\n                        tmp1=parse(occ[spin],l[i])\r\n                        orblist[spin].append(tmp1)\r\n                    elif l[i]=='to':\r\n                        tmp1,tmp2=parse(occ[spin],l[i-1]),parse(occ[spin],l[i+1])\r\n                        for j in range(abs(tmp1-tmp2)-1):\r\n                            orblist[spin].append(1+j+min(tmp1,tmp2))\r\n                    elif i==0 and (l[i]=='a' or l[i]=='b'):\r\n                        pass\r\n                    else:\r\n                        print('Error in input! Exit program')\r\n                        exit()\r\n    read.close()\r\n    aorblist,borblist=orblist[0],orblist[1]\r\n    aorblist.sort(),borblist.sort()\r\n    return aorblist,borblist\r\n\r\ndef list_ene(output,listfile,writefile):\r\n    aocc,avir=orb_ene(output,0)\r\n    aorb=aocc+avir\r\n    bocc,bvir=orb_ene(output,1)\r\n    borb=bocc+bvir\r\n    occ=[aocc,bocc]\r\n    vir=[avir,bvir]\r\n    orb=[aorb,borb]\r\n    smallab,bigab=['a','b'],['Alpha','Beta']\r\n    orblist=relist(occ,listfile)\r\n    with open(writefile,'w') as ene:\r\n        for spin in range(2):\r\n            if len(bocc)==0 and spin==1:\r\n                break\r\n            orbs=orb[spin]\r\n            ene.write(bigab[spin]+'-HOMO is orbital '+str(len(occ[spin]))+smallab[spin]+'\\n')\r\n            gap=float(orbs[len(occ[spin])])-float(orbs[len(occ[spin])-1])\r\n            ene.write(bigab[spin]+'-HOMO-LUMO gap is '+format(gap,'.5f')+' a.u. or '+format(gap*27.2114,'.5f')+' eV\\n')\r\n            for i in range(len(orblist[spin])):\r\n                orbene_au=orbs[orblist[spin][i]-1]\r\n                orbene_ev=format(float(orbene_au)*27.2114,'.5f')\r\n                ene.write(str(orblist[spin][i])+smallab[spin]+'\\t'+orbene_au+'\\t'+orbene_ev+'\\n')\r\n            ene.write('\\n')\r\n    ene.close()\r\n    return\r\n\r\noutput=sys.argv[1]\r\nlistfile='orblist.txt'\r\ntry:\r\n    listfile=sys.argv[2]\r\nexcept:\r\n    pass\r\nwritefile='orbene.txt'\r\ntry:\r\n    writefile=sys.argv[3]\r\nexcept:\r\n    pass\r\nlist_ene(output,listfile,writefile)\r<\/code><\/pre>\n\n\n\n
\u8f93\u51fa\u793a\u4f8b\uff1a<\/p>\n\n\n\n
Alpha-HOMO is orbital 217a\nAlpha-HOMO-LUMO gap is 0.06212 a.u. or 1.69037 eV\n213a\t-0.25040\t-6.81373\n214a\t-0.24144\t-6.56992\n215a\t-0.23823\t-6.48257\n216a\t-0.23769\t-6.46788\n217a\t-0.14421\t-3.92416\n218a\t-0.08209\t-2.23378\n219a\t-0.07925\t-2.15650\n220a\t-0.07452\t-2.02779\n221a\t-0.03748\t-1.01988\n222a\t-0.02886\t-0.78532\n\nBeta-HOMO is orbital 215b\nBeta-HOMO-LUMO gap is 0.05099 a.u. or 1.38751 eV\n211b\t-0.24697\t-6.72040\n212b\t-0.24529\t-6.67468\n213b\t-0.23739\t-6.45971\n214b\t-0.23734\t-6.45835\n215b\t-0.23716\t-6.45346\n216b\t-0.18617\t-5.06595\n217b\t-0.07925\t-2.15650\n218b\t-0.07677\t-2.08902\n219b\t-0.07473\t-2.03351\n220b\t-0.07442\t-2.02507<\/code><\/pre>\n\n\n\n
2. \u6279\u91cf\u63d0\u53d6\u5206\u5b50\u8f68\u9053\u80fd\u91cf<\/strong><\/p>\n\n\n\n
\u642d\u914d1\u4e2d\u811a\u672c\u4f7f\u7528\uff0c\u4e00\u6b21\u6027\u83b7\u53d6\u5f53\u524d\u76ee\u5f55\u4e0b\u6240\u6709.log\u6587\u4ef6\u8bb0\u5f55\u7684\u5206\u5b50\u8f68\u9053\u4fe1\u606f\u3002\u5bf9\u4e8e\u4f18\u5316\u4efb\u52a1\uff0c\u9ed8\u8ba4\u83b7\u53d6\u6700\u540e\u4e00\u5e27\u7ed3\u6784\u7684\u4fe1\u606f\u3002<\/p>\n\n\n\n
for i in .\/*.log\r\ndo\r\n  fname=`basename $i .log`\r\n  orbene $i .\/orblist.txt .\/orbene_$fname.txt\r\ndone\r\nmkdir orb_ene\r\nmv .\/orbene_*.txt orb_ene\/<\/code><\/pre>\n\n\n\n
3. \u6279\u91cf\u5bfc\u51fa\u5206\u5b50\u8f68\u9053\u683c\u70b9\u6570\u636e<\/strong><\/p>\n\n\n\n
\u524d\u7ebf\u8f68\u9053\u7684\u5206\u5e03\u662f\u65f6\u5e38\u4f1a\u5173\u5fc3\u7684\u95ee\u9898\uff0c\u4ee5\u4e0b\u811a\u672c\u4f1a\u8c03\u7528Multiwfn\uff08\u5047\u5b9a\u901a\u8fc7mwfn\u547d\u4ee4\u8fd0\u884c\uff09\u4ea7\u751f.cub\u6587\u4ef6\uff0c\u63a5\u53d7\u4e00\u4e2a\u53c2\u6570N\u7528\u4e8e\u5b9a\u4e49\u8f68\u9053\u8303\u56f4\u3002\u4e8b\u5b9e\u4e0a\u4e5f\u53ef\u4ee5\u4e0e1\u4e2d\u811a\u672c\u7ed3\u5408\uff0c\u4f7f\u8f68\u9053\u8303\u56f4\u5b9a\u4e49\u66f4\u4f73\u7075\u6d3b\uff0c\u4e0d\u8fc7\u4e00\u822c\u6211\u4eec\u53ea\u5173\u5fc3\u524d\u7ebf\u8f68\u9053\uff0c\u4f7f\u7528\u4e00\u4e2a\u53c2\u6570\u5b9a\u4e49\u5df2\u7ecf\u8db3\u591f\u3002<\/p>\n\n\n\n
\u4f7f\u7528\u65b9\u6cd5\uff1a.\/FMO.sh N\uff08\u4ea7\u751fHOMO-(N-1)\u81f3LUMO-(N-1)\u8303\u56f4\u7684\u5206\u5b50\u8f68\u9053\u683c\u70b9\u6570\u636e\uff09<\/p>\n\n\n\n
function judge_u(){\n  mwfn $1 > .\/null << EOF\nq\nEOF\n  set `grep 'determinant' .\/null`\n  rm -f .\/null\n  if [ $4 = 'unrestricted' ]\n  then\n    return 1\n  else\n    return 0\n  fi\n}\n\nfunction get_orb(){\n  mwfn $1 > .\/null << EOF\n200\n3\n$2\n3\n0\nq\nEOF\n  rm -f .\/null\n}\n\nmkdir fmos\nfor i in .\/*fchk\ndo\n  fname=`basename $i .fchk`\n  mkdir fmos\/$fname\n\n  judge_u $i\n  if [ $? = 0 ]\n  then\n    get_orb $i h\n    get_orb $i l\n    j=1\n    while ((j<$1))\n    do\n      get_orb $i h-$j\n      get_orb $i l+$j\n      ((j++))\n    done\n  else\n    for s in {a,b}\n    do\n      get_orb $i h$s\n      get_orb $i l$s\n      j=1\n      while ((j<$1))\n      do\n        get_orb $i h$s-$j\n        get_orb $i l$s+$j\n        ((j++))\n      done\n    done\n  fi\n\n  mv .\/*.cub fmos\/$fname\ndone<\/code><\/pre>\n\n\n\n
4. \u6279\u91cf\u6e32\u67d3\u5206\u5b50\u8f68\u9053\u7b49\u503c\u9762\u56fe<\/strong><\/p>\n\n\n\n
\u8be5\u811a\u672c\u9700\u8981\u5b89\u88c5VMD1.9.3\u548cvcube2.0\uff0c\u53ef\u4ecehttp:\/\/bbs.keinsci.com\/thread-18150-1-1.html<\/a>\u4e0b\u8f7d\u3002\u8fd0\u884c\u540e\u81ea\u52a8\u8c03\u7528VMD\u548cvcube\uff0c\u4f7f\u7528Tachyon\u6e32\u67d3\u5668\u8fdb\u884c\u6279\u91cf\u6e32\u67d3\u3002\u9700\u8981\u5f53\u524d\u76ee\u5f55\u4e0b\u6709\u4e00\u4e2ashow.tcl\u6587\u4ef6\u7528\u4f5c\u53ef\u89c6\u5316\u6a21\u677f\uff0c\u4f7f\u7528\u65f6\u5148\u5bf9\u4e00\u4e2a\u5206\u5b50\u8fdb\u884c\u8c03\u6574\uff0c\u6548\u679c\u6ee1\u610f\u540e\u5c06\u64cd\u4f5c\u8fc7\u7a0b\u901a\u8fc7VMD\u5bfc\u51fa\u5373\u53ef\u3002<\/p>\n\n\n\n
\u4f7f\u7528\u65b9\u6cd5\uff1a.\/MO_Isosurface.sh<\/p>\n\n\n\n
for i in .\/*.cub\r\ndo\r\n  fname=`basename $i .cub`\r\n  vmd << EOF\r\nvmol $i\r\n`cat .\/show.tcl`\r\nvrender\r\nn\r\nquit\r\nEOF\r\n  rm -f .\/VCUBE\/renderall.bat .\/VCUBE\/renderall.sh\r\n  mv .\/VCUBE\/renderall.dat $fname.dat\r\ndone\r\n\r\ncd .\/VCUBE\r\nfor i in .\/*.dat\r\ndo\r\n  \/usr\/local\/lib\/vmd\/tachyon_LINUXAMD64 $i -format BMP -o $i.bmp -trans_raster3d -res 2000 1500 -numthreads 16 -aasamples 24 -mediumshade\r\ndone\r\ncd ..<\/code><\/pre>\n","protected":false},"excerpt":{"rendered":"
\u5206\u5b50\u8f68\u9053\u5904\u7406\u61d2\u4eba\u811a\u672cOne-Key Researc …<\/p>\n","protected":false},"author":9,"featured_media":0,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"spay_email":"","footnotes":""},"categories":[5],"tags":[],"class_list":["post-552","post","type-post","status-publish","format-standard","hentry","category-computchem"],"jetpack_featured_media_url":"","_links":{"self":[{"href":"https:\/\/www.homechemer.com\/index.php?rest_route=\/wp\/v2\/posts\/552","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.homechemer.com\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.homechemer.com\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.homechemer.com\/index.php?rest_route=\/wp\/v2\/users\/9"}],"replies":[{"embeddable":true,"href":"https:\/\/www.homechemer.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=552"}],"version-history":[{"count":2,"href":"https:\/\/www.homechemer.com\/index.php?rest_route=\/wp\/v2\/posts\/552\/revisions"}],"predecessor-version":[{"id":555,"href":"https:\/\/www.homechemer.com\/index.php?rest_route=\/wp\/v2\/posts\/552\/revisions\/555"}],"wp:attachment":[{"href":"https:\/\/www.homechemer.com\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=552"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.homechemer.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=552"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.homechemer.com\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=552"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}