|
| 1 | +--- |
| 2 | +layout: default |
| 3 | +title: MECP Screening |
| 4 | +parent: "MECP Calculations" |
| 5 | +grand_parent: "Examples and Guides" |
| 6 | +nav_order: 2 |
| 7 | +toc: false |
| 8 | +summary: "(Semi-automated) Screening of benzene MECPs with GFN2-xTB" |
| 9 | +permalink: /page/examples/mecp/mecp_screen.html |
| 10 | +--- |
| 11 | + |
| 12 | +# {{page.title}} |
| 13 | +{: .no_toc } |
| 14 | + |
| 15 | +{{ page.summary }} |
| 16 | +{: .fs-6 .fw-300 } |
| 17 | + |
| 18 | +<div class="label label-green">CREST 3.0 preview</div> |
| 19 | + |
| 20 | + |
| 21 | +--- |
| 22 | + |
| 23 | +## (Semi-automated) Screening of benzene MECPs with GFN2-xTB |
| 24 | + |
| 25 | +An extension of the [minimum energy crossing point optimization](mecp_opt.html "Examples / MECP Optimization"), is the |
| 26 | +metadynamics-based screening (analogously to conformational sampling). |
| 27 | +It can be called *via* the new [**input file reader** {{site.data.icons.book}}](../documentation/inputfiles.html "Documentation / Input Files"). |
| 28 | +Again, for the GFN2-xTB *S*<sub>0</sub>/*T*<sub>1</sub> MECPs of benzene: |
| 29 | +{: .text-justify } |
| 30 | + |
| 31 | + <!-- Tab links --> |
| 32 | +<div class="tab card"> |
| 33 | + <button class="tablinks tab-id-1" onclick="openTabId(event, 'tab-1-1', 'tab-id-1')" id="open-1">{{ site.data.icons.code }} <code>command</code></button> |
| 34 | + <button class="tablinks tab-id-1" onclick="openTabId(event, 'tab-1-2', 'tab-id-1')">{{ site.data.icons.codefile }} <code>struc.xyz</code></button> |
| 35 | + <button class="tablinks tab-id-1" onclick="openTabId(event, 'tab-1-3', 'tab-id-1')">{{ site.data. icons.codefile }} <code>input.toml</code></button> |
| 36 | +</div> |
| 37 | +<!-- Tab content --> |
| 38 | +<div id="tab-1-1" class="tabcontent tab-id-1" style="text-align:justify"> |
| 39 | +{% include command.html cmd="crest <span class='nt'>--input</span> input.toml" %} |
| 40 | +</div> |
| 41 | +<div id="tab-1-2" class="tabcontent tab-id-1" style="text-align:justify"> |
| 42 | +{% capture struc_file %} |
| 43 | + 12 |
| 44 | + |
| 45 | + C 1.3830400000 -0.2213700000 0.0054100000 |
| 46 | + C 0.8812100000 1.0799600000 0.0137400000 |
| 47 | + C -0.4965300000 1.2961400000 0.0106300000 |
| 48 | + C -1.3728900000 0.2109800000 -0.0044700000 |
| 49 | + C -0.8710300000 -1.0904600000 -0.0146100000 |
| 50 | + C 0.5067700000 -1.3067000000 -0.0079300000 |
| 51 | + H 2.4566500000 -0.3899700000 0.0090900000 |
| 52 | + H 1.5639800000 1.9254500000 0.0228700000 |
| 53 | + H -0.8876100000 2.3099700000 0.0197800000 |
| 54 | + H -2.4463500000 0.3796100000 -0.0082500000 |
| 55 | + H -1.5536800000 -1.9359000000 -0.0272900000 |
| 56 | + H 0.8977800000 -2.3206600000 -0.0132700000 |
| 57 | +{% endcapture %} |
| 58 | +{% include codecell.html content=struc_file style="font-size:10px" %} |
| 59 | +</div> |
| 60 | +<div id="tab-1-3" class="tabcontent tab-id-1" style="text-align:justify"> |
| 61 | +{% capture toml_file %} |
| 62 | +#This is a CREST input file |
| 63 | +input = 'struc.xyz' |
| 64 | +runtype='mecp_search' # MECP sampling runtype |
| 65 | + |
| 66 | +#parallelization |
| 67 | +threads = 10 |
| 68 | + |
| 69 | +#calculation data |
| 70 | +[calculation] |
| 71 | +eprint = true |
| 72 | +elog="energies.log" |
| 73 | + |
| 74 | +[[calculation.mecp]] # This block automatically sets up a uhf=0 and uhf=2 calculation with xtb |
| 75 | +method = "xtb" |
| 76 | +prog = "xtb" |
| 77 | +flags = "--gfn 2 --grad" |
| 78 | + |
| 79 | +[[calculation.constraints]] |
| 80 | +gapdiff2 = [7.5, 0.005, 0.25] |
| 81 | + |
| 82 | +#molecular dynamics data, required for MECP sampling runtype |
| 83 | +[dynamics] |
| 84 | +length = 10.0 |
| 85 | +tstep = 2.5 |
| 86 | +dump = 100.0 |
| 87 | +hmass = 4 |
| 88 | + |
| 89 | +{% endcapture %} |
| 90 | +{% include codecell.html content=toml_file style="font-size:10px" %} |
| 91 | +</div> |
| 92 | +{% include defaulttab.html id="open-1" %} |
| 93 | + |
| 94 | +The sampling algorithm will run in parallel several (*i.e.*, ten) metadynamics simulations *on the mixed PES including the gap potential* and MECP-optimize the output trajectories. |
| 95 | +While the metadynamics bias potentials are set up automatically, **the user is responsible for setting the MD parameters**, such as the simulation lengths in *ps*. |
| 96 | +Some benzene MECPs that can be found with this method are shown below (in comparison with FOMO-CASCI(6,5) structures in transparent blue). |
| 97 | +{: .text-justify } |
| 98 | + |
| 99 | +{% include image.html file="example-mecp-2.png" alt="Benzene MECPs" caption="Some GFN2-xTB S<sub>0</sub>/T<sub>1</sub> MECPs for benzene, found with semi-automated metadynamics sampling. Transparent blue are FOMO-CASCI(6,5) reference structures." max-width=700%} |
| 100 | + |
| 101 | + |
0 commit comments