{"id":1481,"date":"2024-05-09T07:58:31","date_gmt":"2024-05-08T23:58:31","guid":{"rendered":"https:\/\/www.homechemer.com\/?p=1481"},"modified":"2024-05-09T08:14:59","modified_gmt":"2024-05-09T00:14:59","slug":"gau_chemsh-py-tcl-chemshell%e8%b0%83%e7%94%a8gaussian%e4%bc%98%e5%8c%96%e5%99%a8","status":"publish","type":"post","link":"https:\/\/www.homechemer.com\/computchem\/12","title":{"rendered":"gau_chemsh.py: Tcl-ChemShell\u8c03\u7528Gaussian\u4f18\u5316\u5668"},"content":{"rendered":"\n

gau_chemsh.py: Tcl-ChemShell\u8c03\u7528Gaussian\u4f18\u5316\u5668
gau_chemsh.py: Enabling Tcl-ChemShell Using Gaussian Optimizer<\/strong><\/p>\n\n\n\n

Jiawei Xu
Released: 2024-05-09 \/ Updated: 2024-05-09<\/p>\n\n\n\n

Tcl-ChemShell\uff08\u4ee5\u4e0b\u7b80\u79f0chemsh\uff09\u662f\u5e38\u7528\u7684QM\/MM\u8ba1\u7b97\u63a5\u53e3\u7a0b\u5e8f\u3002\u9ed8\u8ba4\u60c5\u51b5\u4e0b\uff0cchemsh\u4f7f\u7528DL-find\u4f5c\u4e3a\u4f18\u5316\u5668\u3002chemsh\u652f\u6301\u505a\u6781\u5c0f\u70b9\u4f18\u5316\u3001\u4f7f\u7528dimer\u6216NEB (nudged elastic band)\u65b9\u6cd5\u505a\u8fc7\u6e21\u6001\u641c\u7d22\uff0c\u4ee5\u53ca\u6700\u4f4e\u80fd\u91cf\u8def\u5f84(minimum energy path, MEP)\u641c\u7d22\u3002\u5b9e\u8df5\u8bc1\u660e\uff0c\u867d\u7136\u4e00\u822c\u8ba4\u4e3adimer\u65b9\u6cd5\u505a\u8fc7\u6e21\u6001\u641c\u7d22\u662f\u5f88\u9ad8\u6548\u7684\uff0c\u4f46\u5176\u7ed3\u679c\u5bf9\u521d\u59cb\u7ed3\u6784\u8981\u6c42\u6bd4\u8f83\u9ad8\uff0c\u5bf9\u4e8e\u590d\u6742\u4f53\u7cfb\u4e00\u822c\u9700\u8981\u901a\u8fc7\u67d4\u6027\u626b\u63cf\u7ed9\u51fa\u8d77\u59cb\u7684\u4e24\u4e2adimer\u7ed3\u6784\uff0c\u800c\u5931\u8d25\u6982\u7387\u4ecd\u6bd4\u8f83\u9ad8\u3002\u53e6\u5916\uff0cchemsh\u4e0d\u652f\u6301IRC\u8ba1\u7b97\u3002\u672c\u6587\u5c06\u4ecb\u7ecdgau_chemsh.py\u7684\u4f7f\u7528\u65b9\u6cd5\u3002<\/p>\n\n\n\n

1. \u67d4\u6027\u626b\u63cf
<\/strong>chemsh\u6709\u81ea\u5e26\u7684surface\u5173\u952e\u8bcd\u505a\u67d4\u6027\u626b\u63cf\uff0c\u4f46\u6ca1\u6709\u7b80\u4fbf\u7684\u65b9\u6cd5\u53ef\u4ee5\u751f\u6210\u67d4\u6027\u626b\u63cf\u6240\u9700\u7684\u5197\u4f59\u5185\u5750\u6807\u77e9\u9635(z-matrix)\uff0c\u4e5f\u4e0d\u65b9\u4fbf\u6dfb\u52a0\u88ab\u626b\u63cf\u7684\u53d8\u91cf\u3002\u867d\u7136\u53ef\u4ee5\u5728\u8f93\u5165\u6587\u4ef6\u4e2d\u7f16\u5199\u590d\u6742\u7684tcl\u811a\u672c\u7528\u4e8e\u66f4\u65b0\u7ed3\u6784\uff0c\u4f46\u8fd9\u53ea\u9002\u7528\u4e8e\u5904\u7406\u88ab\u626b\u63cf\u53d8\u91cf\u662f\u539f\u5b50\u8ddd\u79bb\u7684\u60c5\u51b5\uff0c\u65e0\u6cd5\u5904\u7406\u66f4\u590d\u6742\u7684\u7ed3\u6784\u53d8\u91cf\u3002\u672c\u4f8b\u6211\u4eec\u4ecb\u7ecd\u4f7f\u7528gau_chemsh.py\u4e3achemsh\u8c03\u7528Gaussian\u4f18\u5316\u5668\u505a\u67d4\u6027\u626b\u63cf\u8ba1\u7b97\u7684\u65b9\u6cd5\u3002\u6240\u7528\u8f6f\u4ef6\u7248\u672c\u4e3aTcl-ChemShell 3.7.1\u548cGaussian16 Revision C.01\u3002
1.1 \u8f93\u5165\u6587\u4ef6<\/strong>
\u6211\u4eec\u4f7f\u7528chemsh\u4f5c\u4e3aORCA\u548cDL_poly\u7684\u63a5\u53e3\uff0c\u5176\u4e2d\u53c2\u6570\u4f7f\u7528AMBER\u683c\u5f0f\u3002\u51c6\u5907chemsh\u505aQM\/MM\u8ba1\u7b97\u6240\u5fc5\u987b\u7684\u8f93\u5165\u6587\u4ef6scan.c\u3001scan.prmtop\u548cscan.chm\uff0c\u5176\u4e2dscan.c\u4e3a\u8d77\u59cb\u7ed3\u6784\uff0cscan.prmtop\u4e3a\u6574\u4e2a\u4f53\u7cfb\u7684\u53c2\u6570\u6587\u4ef6\uff1bscan.chm\u4e3achemsh\u8f93\u5165\u6587\u4ef6\u7684\u6a21\u677f\uff0c\u4f46\u4e0d\u5305\u542b\u5177\u4f53\u8ba1\u7b97\u547d\u4ee4\uff0c\u5176\u5177\u4f53\u5185\u5bb9\u5982\u4e0b\uff1a<\/p>\n\n\n\n

set sysname scan
set program \"~\/programs\/orca-5.0.4\/orca\"
source ~\/files\/tools\/orca5.0-chemsh.tcl

set qm_atom_numbers { 1-33 }
set active_atom_numbers { 1-61 }

set qm_charge -2
set qm_mult 1

set orcasimpleinput \"! xtb\"
set orcablocks { %pal nprocs 16 end }

set qmmm [ list \\
           coupling = shift \\
           qm_region = ${qm_atom_numbers} \\
           qm_theory = orca : [ list \\
                                executable = ${program} \\
                                jobname = ${sysname}_orca \\
                                orcasimpleinput = ${orcasimpleinput} \\
                                orcablocks = ${orcablocks} \\
                                charge = ${qm_charge} \\
                                mult = ${qm_mult} ] \\
           mm_theory = dl_poly : [ list \\
                                   amber_prmtop_file = ${sysname}.prmtop \\
                                   exact_srf = yes \\
                                   use_pairlist = no \\
                                   mxlist = 40000 \\
                                   mxexcl = 2000  \\
                                   cutoff = 1000 \\
                                   debug_memory = no \\
                                   scale14 = [ list [ expr 1 \/ 1.2 ] 0.5 ] \\
                                   save_dl_poly_files = yes \\
                                   conn = ${sysname}.c \\
                                   list_option = none ]]<\/code><\/pre>\n\n\n\n
\u4e0a\u8ff0\u5185\u5bb9\u5305\u542b\u4e86\u4f53\u7cfb\u7684\u76f8\u5173\u8bbe\u7f6e\uff0c\u4ee5\u53ca\u53d8\u91cf\u540d\u4e3aqmmm\u7684\u80fd\u91cf\u68af\u5ea6\u65b9\u6cd5\u8bbe\u5b9a\uff0c\u8fd9\u5c06\u88abgau_chemsh.py\u7528\u4e8e\u5728\u5404\u79cd\u8ba1\u7b97\u4efb\u52a1\u4e2d\u8bbe\u5b9a\u201ctheory = hybrid : ${qmmm}\u201d\u3002\u6ce8\u610f\uff0c\u672c\u6a21\u677f\u4e2d\u4f7f\u7528\u201cqm_atom_numbers\u201d\u548c\u201cactive_atom_numbers\u201d\u8bbe\u5b9aQM\u533a\u57df\u548c\u6d3b\u6027\u533a\u57df\u7684\u539f\u5b50\u5e8f\u53f7\uff0c\u8fd9\u4e24\u4e2a\u53d8\u91cf\u540d\u4e0d\u80fd\u6539\u53d8\uff0cgau_chemsh.py\u5c06\u636e\u6b64\u786e\u5b9aQM\u533a\u57df\u548c\u6d3b\u6027\u533a\u57df\u7684\u8303\u56f4\u3002
\u53e6\u5916\u51c6\u5907gau_chemsh.py\u7684\u8f93\u5165\u6587\u4ef6scan.inp\uff0c\u5176\u5177\u4f53\u5185\u5bb9\u5982\u4e0b\uff1a<\/p>\n\n\n\n
# input file for gau_chemsh.py
c0              scan.c          # necessary: input structure
chm             scan.chm        # necessary: chemsh input file template
sysname         scan            # necessary: point to ${sysname}.e, ${sysname}.g and ${sysname}.h<\/code><\/pre>\n\n\n\n
\u4e0a\u8ff0\u8f93\u5165\u6587\u4ef6\u5305\u542b\u4e86\u4e09\u4e2a\u5173\u952e\u8bcd\uff1a(1) c0\uff1a\u6307\u5b9a\u521d\u59cb\u7ed3\u6784\uff1b(2) chm\uff1a\u6307\u5b9achemsh\u8f93\u5165\u6a21\u677f\u6587\u4ef6\uff1b(3) sysname\uff1a\u8bbe\u7f6e\u4f53\u7cfb\u540d\u79f0\uff0c\u8fd9\u5c06\u7528\u4e8e\u4e00\u7cfb\u5217\u6587\u4ef6\u7684\u547d\u540d\u3002\u4e3a\u4e86\u4f7f\u7528\u6237\u4f7f\u7528\u66f4\u4e3a\u7075\u6d3b\uff0cgau_chemsh.py\u4e0d\u4f1a\u4ecechemsh\u6a21\u677f\u6587\u4ef6\u4e2d\u5c1d\u8bd5\u8bfb\u53d6\u521d\u59cb\u7ed3\u6784\u6216\u4f53\u7cfb\u540d\u79f0\uff0c\u56e0\u6b64\u4ee5\u4e0a\u5173\u952e\u8bcd\u90fd\u662f\u5fc5\u987b\u8bbe\u5b9a\u7684\u3002<\/p>\n\n\n\n
1.2 \u67d4\u6027\u626b\u63cf\u8ba1\u7b97<\/strong>
\u5728\u547d\u4ee4\u884c\u4e2d\u8fd0\u884c\uff1apython gau_chemsh.py -i scan.inp –init\uff0c\u751f\u6210\u7528\u4e8eGaussian\u505a\u67d4\u6027\u626b\u63cf\u4efb\u52a1\u7684\u8f93\u5165\u6587\u4ef6scan.gjf\u3002\u9ed8\u8ba4\u4ea7\u751f\u7684\u662f\u505a\u8fc7\u6e21\u6001\u641c\u7d22\u8ba1\u7b97\u7684\u8f93\u5165\u6587\u4ef6\uff0c\u624b\u52a8\u4fee\u6539\u76f8\u5e94\u5173\u952e\u8bcd\uff0c\u5373\u6307\u5b9aopt=modredundant\uff0c\u5e76\u6dfb\u52a0\u88ab\u626b\u63cf\u53d8\u91cf\u7684\u5197\u4f59\u5185\u5750\u6807\u8bbe\u5b9a\u3002\u5bf9\u4e8e\u672c\u4f8b\uff0c\u5176\u5177\u4f53\u5185\u5bb9\u5982\u4e0b\uff1a<\/p>\n\n\n\n
! Tcl-ChemShell TS Task Using Gaussian16 Optimizer
%nprocshared=1
#p opt(modredundant,nomicro) nosymm ugbs
   external=\"python gau_chemsh.py -i scan.inp --main\"

generated by XMECP

0 1
   O        -2.2513047912        -2.6780736895        -0.4004817984
   O        -1.3880971945        -0.5198143980        -0.5873724977
... ...
   O         1.2902934949         3.6770722855         7.7870162694

B 2 9 S 10 0.1

<\/code><\/pre>\n\n\n\n
\u53ef\u4ee5\u6839\u636e\u5b9e\u9645\u9700\u8981\u589e\u51cf\u5173\u952e\u8bcd\u3002\u6ce8\u610f\uff1a\u5982\u679c\u6dfb\u52a0\u4e86calcfc\u3001recalc=n\u6216calcall\uff0cgau_chemsh.py\u4f1a\u6309\u9700\u8fdb\u884c\u4e8c\u9636\u5bfc\u6570\u8ba1\u7b97\uff0c\u4f46chemsh\u4e0d\u652f\u6301\u9759\u7535\u5d4c\u5165\u7684QM\/MM\u89e3\u6790\u4e8c\u9636\u5bfc\u6570\uff0c\u56e0\u6b64\u662f\u8ba1\u7b97\u6570\u503c\u4e8c\u9636\u5bfc\u6570\uff0c\u8017\u65f6\u5f88\u9ad8\uff0cgau_chemsh.py\u9ed8\u8ba4\u53ea\u5bf9QM\u533a\u57df\u539f\u5b50\u8ba1\u7b97\u6570\u503c\u4e8c\u9636\u5bfc\u6570\u3002\u9ed8\u8ba4\u7684\u5173\u952e\u8bcd\u4e2d\uff0cnomicro\u548cnosymm\u4e0d\u80fd\u5220\u53bb\uff0cugbs\u4e0d\u5efa\u8bae\u5220\u53bb\u3002\u53e6\u5916\uff0c\u4e0d\u8981\u4fee\u6539\u5e76\u884c\u6838\u6570\uff0c\u5426\u5219Gaussian\u4f1a\u603b\u662f\u5360\u7528\u4e00\u534a\u7684\u6838\u6570\u800c\u4e0d\u6267\u884c\u4efb\u4f55\u8ba1\u7b97\u3002
\u5982\u679c\u5f53\u524d\u7cfb\u7edf\u4e2d\u4f7f\u7528\u201cpython\u201d\u547d\u4ee4\u6240\u8c03\u7528\u7684python\u4e0d\u9002\u7528\u4e8egau_chemsh.py\uff0c\u4f8b\u5982\u7248\u672c\u8fc7\u4f4e\uff08\u9700\u8981python3\uff09\u6216\u65e0\u76f8\u5173\u5e93\u652f\u6301\u7b49\uff0c\u53ef\u4ee5\u81ea\u884c\u4fee\u6539external\u4e2d\u8fd0\u884cpython\u7684\u547d\u4ee4\uff0c\u4f7f\u4e4b\u5bf9\u5e94\u4e8e\u5408\u9002\u7684python\u53ef\u6267\u884c\u6587\u4ef6\u3002
\u5b8c\u6210\u4ee5\u4e0a\u5de5\u4f5c\u540e\uff0c\u8fd0\u884c\uff1ag16 scan.gjf\uff0c\u5373\u8fdb\u884c\u67d4\u6027\u626b\u63cf\u8ba1\u7b97\u3002\u5bf9\u4e8e\u96c6\u7fa4\u8ba1\u7b97\u7684\u60c5\u51b5\uff0c\u5219\u662f\u63d0\u4ea4\u4e00\u4e2aGaussian\u4f5c\u4e1a\uff0c\u5e76\u6ce8\u610f\u63d0\u4ea4\u961f\u5217\u7cfb\u7edf\u7684\u811a\u672c\u4e2d\u5e94\u5305\u542b\u6240\u6709\u7528\u5230\u8f6f\u4ef6\u7684\u73af\u5883\u53d8\u91cf\uff0c\u5373\u5728\u5355\u72ec\u505a\u76f8\u540cchemsh\u4f5c\u4e1a\u7684\u57fa\u7840\u4e0a\u8fd8\u989d\u5916\u9700\u8981Gaussian\u7684\u73af\u5883\u53d8\u91cf\u3002\u8ba1\u7b97\u5b8c\u6210\u540e\uff0c\u53ef\u4f7f\u7528GaussView\u76f4\u63a5\u67e5\u770b\u67d4\u6027\u626b\u63cf\u7684\u7ed3\u679c\u3002\u8be5\u65b9\u6cd5\u9002\u7528\u4e8e\u626b\u63cf\u952e\u957f\u3001\u952e\u89d2\u548c\u4e8c\u9762\u89d2\uff0c\u4e5f\u9002\u7528\u4e8e\u505a\u5404\u79cd\u9650\u5236\u6027\u4f18\u5316\u3002\u5bf9\u4e8eGaussian16 A.03\u53ca\u4ee5\u540e\u7248\u672c\uff0c\u8fd8\u53ef\u4ee5\u901a\u8fc7\u5b9a\u4e49\u5e7f\u4e49\u5185\u5750\u6807(generalized internal coordinate, GIC)\u6765\u5f15\u5165\u66f4\u4e3a\u590d\u6742\u7684\u7ed3\u6784\u53d8\u91cf\uff0c\u4f8b\u5982\u4e24\u4e2a\u82b3\u9999\u73af\u4e4b\u95f4\u7684\u8ddd\u79bb\u3001\u4e24\u4e2a\u5206\u5b50\u8d28\u5fc3\u4e4b\u95f4\u7684\u8ddd\u79bb\u7b49\u3002<\/p>\n","protected":false},"excerpt":{"rendered":"
gau_chemsh.py: Tcl-ChemSh …<\/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-1481","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\/1481","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=1481"}],"version-history":[{"count":4,"href":"https:\/\/www.homechemer.com\/index.php?rest_route=\/wp\/v2\/posts\/1481\/revisions"}],"predecessor-version":[{"id":1485,"href":"https:\/\/www.homechemer.com\/index.php?rest_route=\/wp\/v2\/posts\/1481\/revisions\/1485"}],"wp:attachment":[{"href":"https:\/\/www.homechemer.com\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=1481"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.homechemer.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=1481"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.homechemer.com\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=1481"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}