{"id":643,"date":"2023-06-12T18:54:32","date_gmt":"2023-06-12T10:54:32","guid":{"rendered":"https:\/\/www.homechemer.com\/?p=643"},"modified":"2023-06-12T19:07:22","modified_gmt":"2023-06-12T11:07:22","slug":"%e4%bd%bf%e7%94%a8fcclasses3%e7%a8%8b%e5%ba%8f%e8%ae%a1%e7%ae%97%e7%b3%bb%e9%97%b4%e7%aa%9c%e8%b6%8a%e9%80%9f%e7%8e%87","status":"publish","type":"post","link":"https:\/\/www.homechemer.com\/computchem\/9","title":{"rendered":"\u4f7f\u7528FCClasses3\u7a0b\u5e8f\u8ba1\u7b97\u7cfb\u95f4\u7a9c\u8d8a\u901f\u7387"},"content":{"rendered":"\n

\u4f7f\u7528FCClasses3\u7a0b\u5e8f\u8ba1\u7b97\u7cfb\u95f4\u7a9c\u8d8a\u901f\u7387
Calculating Intersystem Crossing Rate via FCClasses3 Program<\/strong><\/p>\n\n\n\n

Jiawei Xu
Released: 2023-06-12 \/ Updated: 2023-06-12<\/p>\n\n\n\n

\u8ba1\u7b97\u7cfb\u95f4\u7a9c\u8d8a(Intersystem Crossing, ISC)\u901f\u7387\u662f\u51c6\u786e\u8003\u5bdf\u591a\u6001\u53cd\u5e94\u673a\u7406\u7684\u5173\u952e\u4e4b\u4e00\uff0c\u5176\u65b9\u6cd5\u5e76\u4e0d\u552f\u4e00\u3002\u672c\u6587\u5c06\u4ecb\u7ecd\u7531\u610f\u5927\u5229\u91d1\u5c5e\u6709\u673a\u5316\u5b66\u7814\u7a76\u6240Fabrizio Santoro\u7b49\u5f00\u53d1\u7684FCClasses\u7a0b\u5e8f\u7684\u5b89\u88c5\u4ee5\u53ca\u8ba1\u7b97ISC\u901f\u7387\u7684\u65b9\u6cd5\u3002<\/p>\n\n\n\n

1. \u7a0b\u5e8f\u5b89\u88c5<\/strong><\/p>\n\n\n\n

FCClasses\u7684\u6700\u65b0\u7248\u672c\u4e3a3.0.1\uff0c\u53ef\u5728http:\/\/www.iccom.cnr.it\/en\/fcclasses<\/a>\u767b\u8bb0\u5e76\u4e0b\u8f7d\u7a0b\u5e8f\u6e90\u4ee3\u7801\u548c\u624b\u518c\u3002FCClasses3\u662fFortran\u5199\u7684\uff0c\u9700\u8981gfortran\u6216ifort\u7f16\u8bd1\u5668\uff0c\u652f\u6301LaPack\u6216MKL\u6570\u5b66\u5e93\uff0c\u9ed8\u8ba4\u4f7f\u7528LaPack\uff0c\u540c\u65f6\u53ef\u9009FFTW\u5feb\u901f\u5085\u7acb\u53f6\u53d8\u6362\u5e93\u3002<\/p>\n\n\n\n

tar -xf fcclasses3-3.0.1.tar.gz\nmkdir fcclasses3\ncd fcclasses3-3.0.1\n.\/configure --prefix=\/home\/jwxu\/programs\/fcclasses3 --with-mkl --with-fftw (\u5982\u4e0d\u4f7f\u7528MKL\u6216FFTW\uff0c\u4e0d\u5199\u5373\u53ef)\nmake -j && make install -j\nmake test\ncd ..\nrm -rf fcclasses3-3.0.1*<\/code><\/pre>\n\n\n\n
make test\u540e\u4f1a\u8fd0\u884c\u4e00\u7cfb\u5217\u4efb\u52a1\u68c0\u67e5\u662f\u5426\u5b89\u88c5\u6b63\u786e\uff0c\u4e00\u822c\u4e0d\u9700\u8981\u5168\u90e8\u8fd0\u884c\u5b8c\uff0c\u5982\u524d\u51e0\u4e2a\u4efb\u52a1\u90fd\u663e\u793a\u6210\u529f\u8fd0\u884c\uff0c\u5c31\u53ef\u4ee5\u7ed3\u675f\u6d4b\u8bd5\u3002\u5b89\u88c5\u5b8c\u6210\u540e\uff0c\u6240\u6709\u7684\u53ef\u6267\u884c\u6587\u4ef6\u90fd\u5728\/home\/jwxu\/programs\/fcclasses3\/bin\u4e0b\uff0c\u5e76\u9700\u8981\u5728.bashrc\u4e2d\u6dfb\u52a0\u73af\u5883\u53d8\u91cf\uff1aexport PATH=$PATH:\/home\/jwxu\/programs\/fcclasses3\/bin\u3002FCClasses\u7684\u7edd\u5927\u591a\u6570\u4efb\u52a1\u90fd\u53ef\u4ee5\u76f4\u63a5\u5728\u767b\u9646\u8282\u70b9\u4e0a\u8fd0\u884c\u3002<\/p>\n\n\n\n
2. \u8ba1\u7b97\u7cfb\u95f4\u7a9c\u8d8a\u901f\u7387<\/strong><\/p>\n\n\n\n
\u4ee5S1-T1\u4e4b\u95f4\u7684\u7cfb\u95f4\u7a9c\u8d8a\u8fc7\u7a0b\u4e3a\u4f8b\uff0c\u9996\u5148\u901a\u8fc7Gaussian16\u8fdb\u884c\u6784\u578b\u4f18\u5316\u548c\u9891\u7387\u8ba1\u7b97\uff0c\u5f97\u5230.fchk\u6587\u4ef6\u3002FCClasses\u9700\u8981\u63d0\u4f9b\u7ed3\u6784\u3001\u68af\u5ea6\u548cHessian\u77e9\u9635\u4fe1\u606f\uff0c\u7531\u5176\u81ea\u5e26\u7684\u811a\u672c\u53ef\u4ee5\u751f\u6210\u5bf9\u5e94\u683c\u5f0f\u7684\u8f93\u5165\u6587\u4ef6\uff1a<\/p>\n\n\n\n
gen_fcc_state -i S1.fchk\ngen_fcc_state -i T1.fchk<\/code><\/pre>\n\n\n\n
\u4ee5\u4e0a\u547d\u4ee4\u4ea7\u751f\u4e86S1.fcc\u548cT1.fcc\u4e24\u4e2a\u6587\u4ef6\u3002\u51c6\u5907\u4ee5\u4e0b\u8f93\u5165\u6587\u4ef6fcc.inp\uff1a<\/p>\n\n\n\n
$$$\nPROPERTY     =   NR0  ; OPA\/EMI\/ECD\/CPL\/RR\/TPA\/MCD\/IC\nMODEL        =   AH   ; Adiabatic Hessian; AS\/ASF\/AH\/VG\/VGF\/VH\nDE           =   0.150 \uff1b Energy difference in eV\nNR0_COUPL    =   5.00E-6 ; Spin-orbit coupling integral in a.u.\nTEMP         =   298.15 ; Temperature in K\nBROADFUN     =   GAU  ; GAU\/LOR\/VOI\nHWHM         =   0.06 ; Broadening width in eV\nMETHOD       =   TD   ; Time-dependent; TI\/TD\nROT          =   1    ; Rotate state 1\n;VIBRATIONAL ANALYSIS\nNORMALMODES  =   COMPUTE   ; COMPUTE\/READ\/IMPLICIT\nCOORDS       =   CARTESIAN ; CARTESIAN\/INTERNAL\n;INPUT DATA FILES\nSTATE1_FILE  =   S1.fcc\nSTATE2_FILE  =   T1.fcc<\/code><\/pre>\n\n\n\n
\u6ce8\u610f\u4fee\u6539\u8f93\u5165\u6587\u4ef6\u4e2d\u7684\u4e24\u6001\u80fd\u91cf\u5dee\uff08\u672b\u6001\u51cf\u53bb\u521d\u6001\uff09\u4ee5\u53ca\u65cb\u8f68\u8026\u5408\u79ef\u5206\u7684\u6570\u503c\u3002\u7136\u540e\u8fd0\u884c\uff1a<\/p>\n\n\n\n
fcclasses3 fcc.inp<\/code><\/pre>\n\n\n\n
\u8fd0\u884c\u6210\u529f\u540e\u5f97\u5230\u4e00\u7cfb\u5217\u8f93\u51fa\u6587\u4ef6\uff0c\u53ef\u4ecefcc.out\u8bfb\u53d6\u7cfb\u95f4\u7a9c\u8d8a\u901f\u7387\uff0c\u540c\u65f6\u76ee\u5f55\u4e0b\u7684\u5176\u4ed6\u8f93\u51fa\u6587\u4ef6\u8fd8\u63d0\u4f9b\u4e86Huang-Rhys\u56e0\u5b50\u3001Duschinsky\u77e9\u9635\u4ee5\u53ca\u4f4d\u79fb\u77e2\u91cf\u7684\u76f8\u5173\u4fe1\u606f\u3002<\/p>\n\n\n\n
 ========================================================\n Non-radiative rate constant (s-1)  1.425E+08\n (for Ead =    -0.177 eV)\n ========================================================<\/code><\/pre>\n\n\n\n
3. \u4fbf\u6377\u811a\u672c<\/strong><\/p>\n\n\n\n
\u4ee5\u4e0b\u662f\u4e00\u4e2a\u5168\u81ea\u52a8\u8ba1\u7b97ISC\u901f\u7387\u7684\u811a\u672c\uff0c\u53ef\u4f9b\u53c2\u8003\uff1a<\/p>\n\n\n\n
#!\/bin\/bash\n# Usage: .\/runfcc mol1 S1 T1\n\nmol=$1\nstate1=$2\nstate2=$3\n\nexc=\"S1 T2\"\n\nmkdir -p $mol\/fcc-$state1-$state2; cd $mol\/fcc-$state1-$state2\n\n### Generate .fcc inputs\ncp ..\/$state1\/$mol-$state1.chk ..\/$state2\/$mol-$state2.chk .\nfor i in *.chk\ndo\n  name=`basename $i .chk`\n  fchk16 $i $name.fchk\n  gen_fcc_state -i $name.fchk\ndone\nrm *.chk\n\n### Get energy difference\nif [[ \"$exc\" =~ \"$state1\" ]]\nthen\n  set `grep \"E(TD-HF\/TD-DFT)\" ..\/$state1\/$mol-$state1.log | tail -1`\nelse\n  set `grep \"SCF Done\" ..\/$state1\/$mol-$state1.log | tail -1`\nfi\nE1=$5\n\nif [[ \"$exc\" =~ \"$state2\" ]]\nthen\n  set `grep \"E(TD-HF\/TD-DFT)\" ..\/$state2\/$mol-$state2.log | tail -1`\nelse\n  set `grep \"SCF Done\" ..\/$state2\/$mol-$state2.log | tail -1`\nfi\nE2=$5\n\ndE=`echo \"scale=10; ($E2)-($E1)\" | bc`\ndE=`echo \"$dE*27.2114\" | bc`\necho \"The energy difference is $dE eV.\"\n\n### Get spin-orbit coupling integral from DALTON output\ngrep \"B excited state no., symmetry, spin:             ${state1:0-1}\" ..\/..\/dalton\/$state1*dalton\/$mol\/*.out -A 3 -B 2 > null1\ngrep \"C excited state no., symmetry, spin:             ${state2:0-1}\" null1 -A 3 -B 2 > null2\nset `grep X1SPNORB null2 -A 5`; socx=${39}\nset `grep Y1SPNORB null2 -A 5`; socy=${39}\nset `grep Z1SPNORB null2 -A 5`; socz=${39}\n\nsoc2=`echo \"scale=20; ($socx^2)+($socy^2)+($socz^2)\" | bc`\nsoc=`echo \"sqrt($soc2)\" | bc`\nrm null1 null2\necho \"The spin-orbit coupling integral is $soc a.u.\"\n\n### Generate FCClasses main input\nrm -f $mol-fcc-$state1-$state2.inp\ncat >> $mol-fcc-$state1-$state2.inp << EOF\n\\$\\$\\$\nPROPERTY     =   NR0  ; OPA\/EMI\/ECD\/CPL\/RR\/TPA\/MCD\/IC\nMODEL        =   AH   ; AS\/ASF\/AH\/VG\/VGF\/VH\nDE           =   $dE\nNR0_COUPL    =   $soc ; SOC\nTEMP         =   298.15 ; (temperature in K)\nBROADFUN     =   GAU  ; GAU\/LOR\/VOI\nHWHM         =   0.06 ; (broadening width in eV)\nMETHOD       =   TD   ; TI\/TD\nROT          =   1    ; Rotate state 1\n;VIBRATIONAL ANALYSIS\nNORMALMODES  =   COMPUTE   ; COMPUTE\/READ\/IMPLICIT\nCOORDS       =   CARTESIAN ; CARTESIAN\/INTERNAL\n;INPUT DATA FILES\nSTATE1_FILE  =   $mol-$state1.fcc\nSTATE2_FILE  =   $mol-$state2.fcc\nEOF\n\n### Run FCClasses\nfcclasses3 $mol-fcc-$state1-$state2.inp<\/code><\/pre>\n\n\n\n
<\/p>\n\n\n\n
<\/p>\n","protected":false},"excerpt":{"rendered":"
\u4f7f\u7528FCClasses3\u7a0b\u5e8f\u8ba1\u7b97\u7cfb\u95f4\u7a9c\u8d8a\u901f\u7387Cal …<\/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-643","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\/643","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=643"}],"version-history":[{"count":4,"href":"https:\/\/www.homechemer.com\/index.php?rest_route=\/wp\/v2\/posts\/643\/revisions"}],"predecessor-version":[{"id":647,"href":"https:\/\/www.homechemer.com\/index.php?rest_route=\/wp\/v2\/posts\/643\/revisions\/647"}],"wp:attachment":[{"href":"https:\/\/www.homechemer.com\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=643"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.homechemer.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=643"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.homechemer.com\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=643"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}