<div dir="ltr">Thank you so much! Is there any other suggestion on cp2k? Such as some property research on asphalt using ab-initio method?<div><br></div><div>Really appreciate it</div><div>Mason<br><br>在 2014年7月15日星期二UTC-5下午12时55分04秒，ccampana写道：<blockquote class="gmail_quote" style="margin: 0;margin-left: 0.8ex;border-left: 1px #ccc solid;padding-left: 1ex;"><div dir="ltr"><div>Your Q is not so much about CP2K but about reaction chemistry. Reactions are, in principle, rare events thus the likelihood of "seeing" a reaction occurring during an MD run can be null. Due to its stochastic nature, MD is not a great tool to study reaction chemistry. There are cases where MD can be employed to simulate reactions but those are typically systems with a high degree of confinement (relatively dense), highly symmetric or with additional constraints that inhibit certain atomic motions. How to proceed in your case really depends on what you are after but for sure you should be consulting the appropriate textbooks to improve your understanding on the topic. Finding "all the possible products of asphalt oxidation" sounds like a mad quest. If you think all it takes is to drop molecules into a simulation box and "cook" via MD just forget about it. Said this, you may want to check works done with the classical reactive forcefield (reaxff) which has already been used to simulate certain cases of hydrocarbon combustion/oxidation via high temperature MD and/or accelerated MD (<a href="http://pubs.acs.org/doi/abs/10.1021/jp709896w" target="_blank" onmousedown="this.href='http://www.google.com/url?q\75http%3A%2F%2Fpubs.acs.org%2Fdoi%2Fabs%2F10.1021%2Fjp709896w\46sa\75D\46sntz\0751\46usg\75AFQjCNFa-g2C_ndlpfDW060vS9YzjAYu6A';return true;" onclick="this.href='http://www.google.com/url?q\75http%3A%2F%2Fpubs.acs.org%2Fdoi%2Fabs%2F10.1021%2Fjp709896w\46sa\75D\46sntz\0751\46usg\75AFQjCNFa-g2C_ndlpfDW060vS9YzjAYu6A';return true;">http://pubs.acs.org/doi/abs/<wbr>10.1021/jp709896w</a>). Engineers also use reaction kinetic models that solve sets of PDEs to predict reactions species under certain conditions (<a href="http://rmg.mit.edu/" target="_blank" onmousedown="this.href='http://www.google.com/url?q\75http%3A%2F%2Frmg.mit.edu%2F\46sa\75D\46sntz\0751\46usg\75AFQjCNFkUJrqdaWGi0_nvsqYqc-TFrlz5Q';return true;" onclick="this.href='http://www.google.com/url?q\75http%3A%2F%2Frmg.mit.edu%2F\46sa\75D\46sntz\0751\46usg\75AFQjCNFkUJrqdaWGi0_nvsqYqc-TFrlz5Q';return true;">http://rmg.mit.edu/</a>). Keep in mind the aforementioned models rely on many approximations and lack the accuracy of first-principle methods. Yet, they are much faster that the ab-initio ones and sometimes are the only tools to tackle certain problems. As already said, it very much depends on what you are trying to study. I call it a day now.<br>
</div><div>Carlos<br></div><div><br></div><div><br><br><br><br><br><br></div><div><br><br><div class="gmail_quote">On Tue, Jul 15, 2014 at 1:00 PM, C Mason <span dir="ltr"><<a href="javascript:" target="_blank" gdf-obfuscated-mailto="sr0fJe4K910J" onmousedown="this.href='javascript:';return true;" onclick="this.href='javascript:';return true;">bon...@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr">Dear all researchers using cp2k,<div><br></div><div> I'm a pretty new user of cp2k, and still learning functions of this program. I got some questions right now and really need help.</div>
<div> The purpose of my research is to find all the possible products of asphalt oxidation. To begin with, I tried to learn if MD function in cp2k can do simulation of some reactions, and built a simple system containing 2 methanol and 3 oxygen molecules in a 10X10X10 cell. Here's my input file:</div>
<div><br></div><div>Reactions are not observed in 1000 steps. Can someone help me figure out where the problem is?</div><div><br></div><div><div>&FORCE_EVAL</div><div> METHOD QS</div><div> &DFT</div><div> BASIS_SET_FILE_NAME /usr/share/cp2k/BASIS_MOLOPT</div>
<div> POTENTIAL_FILE_NAME /usr/share/cp2k/GTH_POTENTIALS</div><div> &MGRID</div><div> CUTOFF 200</div><div> NGRIDS 4</div><div> &END MGRID</div><div> &QS</div><div> METHOD GAPW</div>
<div> &END QS</div><div> &SCF</div><div> SCF_GUESS RESTART</div><div> MAX_SCF 100</div><div> EPS_SCF 1.0e-6</div><div> &OUTER_SCF</div><div> MAX_SCF 5</div><div> EPS_SCF 1.0E-6</div>
<div> &END</div><div> &OT TRUE</div><div> PRECONDITIONER FULL_ALL</div><div> MINIMIZER CG</div><div> ENERGY_GAP 0.001</div><div> &END OT</div><div> &END SCF</div>
<div> &XC</div><div> &XC_FUNCTIONAL PBE</div><div> &END XC_FUNCTIONAL</div><div> &END XC</div><div> &END DFT</div><div> &SUBSYS</div><div> &CELL</div><div> ABC 10.0 10.0 10.0</div>
<div> &END CELL</div><div>&COORD</div><div>O 5.83970000 2.50019000 2.50074000</div><div>O 4.73464200 2.52884200 2.59250500</div><div>O 5.55838800 3.09963100 7.32479800</div>
<div>O 4.53647400 3.49381100 7.50004500</div><div>O 6.39174700 7.49938300 4.80196400</div><div>O 7.49930100 7.46722100 4.85377500</div><div>C 6.90902000 4.30670800 4.62181700</div>
<div>O 5.64215600 4.88509800 4.49462900</div><div>H 5.20622900 4.78592700 5.38062100</div><div>H 6.81478300 3.23143200 4.88781800</div><div>H 7.49613100 4.83704900 5.40277500</div>
<div>H 7.44563600 4.38928400 3.65434100</div><div>C 3.27312300 5.91737700 3.17814600</div><div>O 4.20868900 6.89713900 3.52519000</div><div>H 4.62313400 7.19318900 2.67346300</div>
<div>H 3.77955300 5.06361100 2.67767800</div><div>H 2.50196900 6.34589000 2.50171900</div><div>H 2.77520500 5.54750300 4.09795900</div><div>&END COORD</div><div> &KIND H</div>
<div> BASIS_SET DZVP-MOLOPT-SR-GTH-q1</div><div> POTENTIAL GTH-PBE-q1</div><div> &END KIND</div><div> &KIND O</div><div> BASIS_SET DZVP-MOLOPT-SR-GTH-q6</div><div> POTENTIAL GTH-PBE-q6</div>
<div> &END KIND</div><div> &KIND C</div><div> BASIS_SET DZVP-MOLOPT-SR-GTH-q4</div><div> POTENTIAL GTH-PBE-q4</div><div> &END KIND</div><div>&END SUBSYS</div><div>&END FORCE_EVAL</div>
<div>&GLOBAL</div><div>PROJECT methanol_try2</div><div> RUN_TYPE MD</div><div>&END GLOBAL</div><div>&MOTION</div><div> &MD</div><div> ENSEMBLE NVT</div><div> STEPS 1000</div><div> TIMESTEP 1.0</div>
<div> TEMPERATURE 800</div><div> TEMP_TOL 100</div><div> &BAROSTAT</div><div> PRESSURE 1000</div><div> &END BAROSTAT</div><div> &THERMOSTAT</div><div> TYPE CSVR</div><div> &CSVR</div>
<div> TIMECON 200</div><div> &END CSVR</div><div> &END THERMOSTAT</div><div> &END MD</div><div>&PRINT</div><div> &TRAJECTORY</div><div> LOG_PRINT_KEY T</div><div> FORMAT XYZ</div>
<div> &EACH</div><div> MD 5</div><div> &END EACH</div><div> ADD_LAST NUMERIC</div><div> &END TRAJECTORY</div><div>&END PRINT</div><div>&END MOTION</div><div>&END</div></div>
<div><br></div><div>Many thanks!</div><span><font color="#888888"><div>Mason</div></font></span></div><span><font color="#888888">
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