Hi Marcella,<div><br /></div><div>Thank you that makes sense, I see the number of CVs do matter, I've replotted using only 2 ndim=ndw and the data looks much better. I can find the minima as well using -find-minima. </div><div><br /></div><div>I also figured out how to make use of the -find-path option by pasting the minima floats obtained from the -find-minima output for -point-a and -point-b, so I'll post it here incase anyone else is wondering.</div><div><br /></div><div>input:</div><div><br />FES| Mapping Gaussians :: 100 %<br />FES| Dumping FES structure in file: < fes.dat ><br /> Iteration nr. 1 1.504066111949192E-002<br /></div><div><br /></div><div>graph.psmp -cp2k -file input.restart -ndim 2 -ndw 1 2 -out fes.dat -find-minima<br /></div><div><br /></div><div>output:</div><div><br /></div><div>FES| Dumping FES structure in file: < fes.dat ><br />FES| Trust hyper-radius 10 10 which is equivalent to: 0.191530 0.483382<br />FES| Minimum found ( 2.727613 2.186932 ). FES value = -0.001262 Hartree. Number of Iter: 102<br />FES| Minimum found ( 3.017643 2.627451 ). FES value = -0.019981 Hartree. Number of Iter: 101<br /></div><div><br /></div><div><br /></div><div>then taking 2 relevant minima and pasting one after another with exact same digits</div><div><br /></div><div><div>graph.psmp -cp2k -file input.restart -ndim 2 -ndw 1 2 -out fes.dat -find-path -point-a 2.727613 2.186932 -point-b 3.017643 2.627451<br /></div><div><br />FES| Mapping Gaussians :: 100 %<br />FES| Dumping FES structure in file: < fes.dat ><br /> Iteration nr. 1 1.504066111949192E-002<br /></div><div>...</div><div>..</div><div> MEP saved on <mep.data> file.<br /><br />FES| NORMAL FES TERMINATION.<br /></div><div><br /></div></div><div>Best regards,</div><div>Liam</div><div><br /></div><div class="gmail_quote"><div dir="auto" class="gmail_attr">On Wednesday, June 28, 2023 at 6:02:03 AM UTC-2:30 Marcella Iannuzzi wrote:<br/></div><blockquote class="gmail_quote" style="margin: 0 0 0 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><div><br></div><div>Dear ...</div><div><br></div>The search of minima using "graph" is possible only considering the whole metadynamics space, no for projections of it to lower dimension.<div>ndw=ndim and ndim should be the actual dimension of the space, otherwise whatever you get is wrong.<br><div>Regards</div><div>Marcella</div><div><br><br></div></div><div class="gmail_quote"><div dir="auto" class="gmail_attr">On Wednesday, June 28, 2023 at 1:44:11 AM UTC+2 Liam H wrote:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">More importantly though, since I do have the minima, I'd like to figure how to use the -find-path option.<div><br></div><div><span style="color:rgb(80,0,80)">graph.psmp -cp2k -file input.restart -find-path -ndim 2 -ndw 1 2 -out fes.dat</span></div><div><font color="#500050"><br></font></div><div><font color="#500050">gives the output:</font><br> ABORT in metadyn_tools/graph.F:362 -find-path requires the specification of -po<br> int-a and -point-b !<br><div><br></div><div>So i've attempted a few combinations<br><div><div><span style="color:rgb(80,0,80)">graph.psmp -cp2k -file input.restart -find-path -point-a -point-b -ndim 2 -ndw 1 2 -out fes.dat</span></div><br></div><div>But I haven't been able to find any examples of the particular format for specifying -point-a and -point-b</div><div><br></div><div>ive tried in the format of the COLVAR , specifying XY <span style="color:rgb(80,0,80)">-point-a</span><span style="color:rgb(80,0,80)"> </span> 2.070, 6.416 -point-b 0.248, 3.076</div><div>ive tried XYZ, ive tried without comma, ive tried line number</div><div><br></div><div>If anyone has any information on the format of the <span style="color:rgb(80,0,80)">-find-path -point-a -point-b function it would be very much appreciated!</span></div><div><br><br></div></div></div><div class="gmail_quote"><div dir="auto" class="gmail_attr">On Tuesday, June 27, 2023 at 4:15:45 PM UTC-2:30 Liam H wrote:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">Yes that's right although it seems to work even though I sampled 6 it will work with
-ndim 2 or
-ndim 3,<div><br></div><div>However, the issue i'm having now.. when using the -find-minima command:</div><div><br></div><div>Also this example is with only 3 CV to simplify, still the same issue with 6.</div><div><br></div><div>it works perfectly when using </div><div><span style="color:rgb(80,0,80)"><br></span></div><div><span style="color:rgb(80,0,80)">graph.psmp -cp2k -file input.restart -find-minima -ndim 2 -ndw 1 2 -out fes.dat</span></div><div><font color="#500050"><br></font></div><div><font color="#500050">however if I try the same thing even with the same two CV with -ndim 3, it fails for both -ndw 1 2 and -ndw 1 3</font></div><div><font color="#500050">Here is an example with the output.</font></div><div><font color="#500050"><br></font></div><div><font color="#500050">The data gets plotted but the -find-minima fails, it works when i use -ndim 2 , it finds 9 minima, but in this case then i cannot access CV3 -ndw 1 3</font></div><div><font color="#500050"><br></font></div><div><font color="#500050"><br></font></div><div><span style="color:rgb(80,0,80)">graph.psmp -cp2k -file input.restart -find-minima -ndim 3 -ndw 1 2 -out fes.dat</span><font color="#500050"><br></font></div><div><font color="#500050"><br></font></div><div>FES| Parsing file: <input.restart><br><br>**********************************************************************<br>FES| Parameters for FES:<br><br>FES| NDIM :: 3<br>FES| NWD :: 2<br>FES| HILLS :: 120<br>FES| COLVAR # 1 :: ( 2.070 , 6.416) ( MAPPED)<br>FES| COLVAR # 3 :: ( 0.248 , 3.076) ( MAPPED)<br>FES| COLVAR # 2 :: ( 1.784 , 3.636) (NO MAPPED)<br>FES| NGRID :: 100 100<br>FES| DX :: 0.044 0.029<br>FES| CUTOFF :: .10000E-05<br>**********************************************************************<br><br><br>FES| Computing Free Energy Surface<br>FES| Mapping Gaussians :: 10 %<br>FES| Mapping Gaussians :: 20 %<br>FES| Mapping Gaussians :: 30 %<br>FES| Mapping Gaussians :: 40 %<br>FES| Mapping Gaussians :: 50 %<br>FES| Mapping Gaussians :: 70 %<br>FES| Mapping Gaussians :: 80 %<br>FES| Mapping Gaussians :: 90 %<br>FES| Mapping Gaussians :: 100 %<br>FES| Mapping Gaussians :: 100 %<br>FES| Dumping FES structure in file: < FES10.dat ><br> ABORT in metadyn_tools/graph_methods.F:279 Not implemented for projected FES!<br>forrtl: error (76): Abort trap signal<br><br></div><div class="gmail_quote"><div dir="auto" class="gmail_attr">On Tuesday, June 27, 2023 at 1:55:32 PM UTC-2:30 Marcella Iannuzzi wrote:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div><br></div>Hello,<div><br></div><div>Both are wrong, the dimension of the sampled space is 6 therefore -ndim 6 is the correct input.</div><div>Regards</div><div>Marcella<br><br></div><div class="gmail_quote"><div dir="auto" class="gmail_attr">On Tuesday, June 27, 2023 at 6:01:50 PM UTC+2 Liam H wrote:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">My concern now is that the plot I get using<div><br></div><div><span style="color:rgb(80,0,80)">graph.psmp -cp2k -file input.restart -ndim 2 -ndw 1 2 -out fes.dat</span></div><div><span style="color:rgb(80,0,80)"><br></span></div><div><span style="color:rgb(80,0,80)">Is not identical when doing -ndim 3 and only mapping the first two CV</span></div><div><font color="#500050"><br></font></div><div><span style="color:rgb(80,0,80)">graph.psmp -cp2k -file input.restart -ndim 3 -ndw 1 2 -out fes.dat</span><font color="#500050"><br></font><br></div><div>I am not sure how this could be, raw data itself looks correct but when plotting the surface it isn't the same the minimums and saddlepoint are completely different when plotting the same CV</div><div><br></div><div class="gmail_quote"><div dir="auto" class="gmail_attr">On Tuesday, June 27, 2023 at 1:23:39 PM UTC-2:30 Liam H wrote:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">Nevermind I figured it out, by changing the -ndim to a higher number , it still allows you to map COLVAR -ndw 1 3<div><br></div><div>graph.psmp -cp2k -file input.restart -ndim 2 -ndw 1 3 -out fes.dat <br></div><div>Doesnt work</div><div><br></div><div>graph.psmp -cp2k -file input.restart -ndim 3 -ndw 1 3 -out fes.dat<br></div><div>works</div><div class="gmail_quote"><div dir="auto" class="gmail_attr">On Tuesday, June 27, 2023 at 12:21:45 PM UTC-2:30 Liam H wrote:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">Hello.<div><br></div><div>I have been running metadynamics simulations with multiple colvar, 6 in this case.</div><div><br></div><div>This is because I want to be able to plot different surfaces with different colvar, because I can't visualize a 6 dimensional surface.</div><div><br></div><div>graph.psmp -cp2k -file input.restart -ndim 2 -ndw 1 2 -out fes.dat<br></div><div><br></div><div>This works fine to give me the 3D surface, (cv1,cv2,energy)</div><div>I would like to plot (cv1,cv3,energy) </div><div><br></div><div>but running the command:</div><div>graph.psmp -cp2k -file input.restart -ndim 2 -ndw 1 3 -out fes.dat<br></div><div><br></div><div>Does not work.</div><div><br></div><div>graph.psmp -cp2k -file input.restart -ndim 6 -ndw 1 2 3 4 5 6 -out fes.dat<br></div><div><br></div><div>This works but produces such a massive file its not practical to try and plot the 2d surface..</div><div>Is there any way to specify which cvs to be used in the plot, without plotting them all at once?<br></div><div><br></div><div><br></div></blockquote></div></blockquote></div></blockquote></div></blockquote></div></blockquote></div></blockquote></div></blockquote></div>
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