Recent Questions - Matter Modeling Stack Exchange most recent 30 from mattermodeling.stackexchange.com 2021-12-01T12:20:35Z https://mattermodeling.stackexchange.com/feeds https://creativecommons.org/licenses/by-sa/4.0/rdf https://mattermodeling.stackexchange.com/q/7183 3 physical interpretation of ENCUT and Kpoints Maulesh VALA https://mattermodeling.stackexchange.com/users/4238 2021-12-01T04:39:32Z 2021-12-01T04:39:32Z <p>What are the Physical interpretation of ENCUT and Kpoints in ab initio calculation? As we are doing optimization of ENCUT and kpoints, why do we need to do it? Also, what is the mathematical relation between 1) ENCUT and energy of the system and 2) Kpoint and energy which is usefull in the relaxation process?</p> <p>Thank you in advance.</p> https://mattermodeling.stackexchange.com/q/7182 3 How does the electronic iteration work in VASP relaxation calculation？a change in electron density n？ Kevin https://mattermodeling.stackexchange.com/users/4642 2021-12-01T04:20:57Z 2021-12-01T11:44:07Z <p>I am a beginner using VASP to do material modeling，and I'm confused about the following questions：</p> <ol> <li>How does the electronic iteration work in VASP relaxation calculation?</li> <li>Is electronic iteration in structure optimization and static self-consistent the same?</li> </ol> <p>If they are the same，it seems that there is no need to perform a static self-consistent calculation after structure optimization, because in the last ion step of structure optimization, the calculation converges and atom position will not change further, electronic iteration there is equivalent to electronic iteration in subsequent self-consistent calculation.</p> https://mattermodeling.stackexchange.com/q/7181 3 How to calculate displacement in each coordinate and wrap w.r.t. lattice parameter? Saha_1994 https://mattermodeling.stackexchange.com/users/4219 2021-11-30T20:34:30Z 2021-12-01T10:57:56Z <p>The problem is my box is not orthorhombic (base angles different than 90 degrees). So, I am getting wrong results with the formula,</p> <pre><code>def distance(a, b): dx = abs(a - b) x = min(dx, abs(A - dx)) dy = abs(a - b) y = min(dy, abs(B - dy)) dz = abs(a - b) z = min(dz, abs(C - dz)) return sp.sqrt(x**2 + y**2 + z**2) </code></pre> <p>Any suggestion on how to get the proper distance between any atom and its neighbours, including the periodic images of the neighbours. Basically, it makes the results of RDF and CN unphysical.</p> <p><a href="https://i.stack.imgur.com/jO0ow.png" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/jO0ow.png" alt="enter image description here" /></a></p> https://mattermodeling.stackexchange.com/q/7178 6 Unit Cell Parameters for VASP Calculations Lazarus98 https://mattermodeling.stackexchange.com/users/1441 2021-11-30T03:37:58Z 2021-11-30T13:05:19Z <p>For background, I have never used VASP before and have limited knowledge of how the software works. I am working on a program for the automation of structural creation for 2D materials. I am more of a computer scientist then a computational chemist and someone else is employing all my programs for their VASP optimizations and band width calculations.</p> <p>Currently, my program takes in coordinates for metal centers, organic linkers, etc... and, along with some other user defined parameters, writes a .xyz file for the desired periodic structure. The coordinates from my program are extracted and another program (that I did not write) uses them to write a POSCAR file. However, when the periodic structure is visualized in VESTA with the unit cell vertices, the structure is not centered in the unit cell. At this point, I was asked to make a series of geometrical transformations to the original file in order to get the structure to the desired location.</p> <p>I proposed that we adjust the lattice vectors/parameters to center it based off of the periodic structure coordinates as opposed to using the same lattice parameters and transforming each structure individually, as the former might be more efficient. However, I was told that this is not possible.</p> <p><em><strong>Here is my question</strong></em></p> <p>Is it possible to define the vertices of the unit cell around the structural coordinates?</p> <p>If the situation or question is unclear, I can try and explain it better with diagrams or pictures, however, I apologize in advance as my knowledge in this subject is very limited.</p> <p><strong>EDIT:</strong></p> <p>I did not make these in VASP or VESTA but just made some pictures in Microsoft word to represent the situation as I don't have access to my lab computer right now. Hopefully this makes the question more clear.</p> <p><a href="https://i.stack.imgur.com/a454o.png" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/a454o.png" alt="enter image description here" /></a></p> <p>It initially looks like this when the structure and unit cell vertices are rendered in VESTA. Then, after essentially doing guess and check transformations with the original .xyz file, the structure is transformed to look like this.</p> <p><a href="https://i.stack.imgur.com/IXxv4.png" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/IXxv4.png" alt="enter image description here" /></a></p> <p>So instead of transforming the initial structure, is it possible to change the origin of the basis set for the unit cell vertices (i.e. move the box down and center it based off of the initial molecular coordinates provide.</p> https://mattermodeling.stackexchange.com/q/7169 7 Should one consider the spatial degeneracies of the electronic state while calculating the Gibbs free energy? wzkchem5 https://mattermodeling.stackexchange.com/users/838 2021-11-29T16:20:59Z 2021-11-29T16:20:59Z <p>The Gibbs free energy of a molecule is generally expressed as a sum of translational, rotational, vibrational, electronic and nuclear contributions. The electronic contribution <span class="math-container">$G_{elec}$</span> is formally a sum of Boltzmann factors of all possible electronic states of the system, but since the first electronic excitation energy is usually much larger than <span class="math-container">$kT$</span>, many programs make the approximation <span class="math-container">$G_{elec} = -RT \ln g_0$</span>, where <span class="math-container">$g_0$</span> is the degree of degeneracy of the ground state. For non-relativistic calculations of spatially non-degenerate states, <span class="math-container">$g_0$</span> is simply the spin multiplicity <span class="math-container">$2S+1$</span>. In this case the program can easily choose the correct <span class="math-container">$g_0$</span> automatically, without intervention by the user.</p> <p>However, during our recent development of the BDF software (<a href="http://182.92.69.169:7226/Introduction" rel="noreferrer">http://182.92.69.169:7226/Introduction</a>), I realized that the determination of <span class="math-container">$g_0$</span> in BDF is much more complicated than simply equating it to <span class="math-container">$2S+1$</span>. The reason is that BDF is known for its accurate relativistic methods and full consideration of spatial symmetry, including double-group symmetry. Consequently, compared to other programs, a disproportionately high number of BDF users routinely perform calculations that take into account spin-orbit coupling, where the degree of degeneracy is <span class="math-container">$2J+1$</span> instead of <span class="math-container">$2S+1$</span>, and a considerable number of users also calculate spatially degenerate electronic states.</p> <p>My question is about the latter case. If the electronic state is spatially degenerate, say we are calculating the Gibbs free energy of the triply degenerate <span class="math-container">$1^3P$</span> state of the carbon atom, should we also take the spatial degeneracy of the state into account (i.e. in this case we have <span class="math-container">$g_0=9$</span> instead of <span class="math-container">$g_0=3$</span>)?</p> <p>Theoretically it seems that the answer is yes, but if the electronic structure method used in calculating the electronic energy of the system breaks the spatial symmetry, then the consideration of spatial symmetry may lead to inconsistencies. For example, if the aforementioned carbon atom is computed at the DFT level, then the spherical rotational symmetry of the atom is broken, so that if we compute the excited states of the carbon atom at the same level using TDDFT, we will find that the other two components of the triply degenerate <span class="math-container">$1^3P$</span> state lie quite a bit above the ground state, and a sum of Boltzmann factors will yield a nearly zero spatial contribution to the electronic Gibbs free energy, instead of the expected <span class="math-container">$-RT \ln 3$</span>. Therefore, choosing <span class="math-container">$g_0=9$</span> in this case amounts to taking into account a degeneracy that exists in reality but does not exist in the approximate computational method that we are using, which does not sound entirely satisfactory. Moreover, the consideration of spatial symmetry in this case makes the automatic determination of <span class="math-container">$g_0$</span> very difficult, as the program has to deduce that the true spectral term of the carbon atom is <span class="math-container">$1^3P$</span>, even though the DFT wavefunction has only <span class="math-container">$D_{\infty h}$</span> symmetry.</p> <p>On the practical side, the latter problem means that in all quantum chemistry programs that I know of, a <span class="math-container">$1^3P$</span> carbon atom computed at the DFT level is treated as if it is spatially non-degenerate (at least the degeneracy does not enter the partition function). But I don't know if the user is supposed to manually correct for this. If no, then what about the calculations where the atom is treated by a method that does respect the spatial symmetry, like state-averaged CASSCF? To the best of my knowledge, many (if not all) quantum chemistry programs do not take into account the spatial degree of degeneracy even in this case, but again I don't know if the user has the responsibility to manually add the spatial contribution to the electronic Gibbs free energy.</p> <p>Thank you very much in advance.</p> https://mattermodeling.stackexchange.com/q/7166 8 Confused about the application/definition of improper torsions Roshan Shrestha https://mattermodeling.stackexchange.com/users/1791 2021-11-29T08:53:46Z 2021-11-30T01:13:29Z <p>The only basic definition of improper torsion/improper dihedral I have is - improper dihedral is formed when we have a central atom bonded to the three atoms. Can anyone help me visualize/help to understand how these improper dihedrals help to maintain the planar structure of let's say - benzene?</p> https://mattermodeling.stackexchange.com/q/7165 5 How do you perform parallelization of NEB-TS in ORCA? カイル https://mattermodeling.stackexchange.com/users/4634 2021-11-29T08:26:32Z 2021-11-29T13:22:51Z <p>I have tried running a NEB-TS calculation in orca with <code>%pal nprocs 32</code>, but I get an error saying <code>Parallel child processes not implemented yet</code>. However, when I use <code>nprocs 15</code>, the calculation runs smoothly.</p> <p>I use ORCA 4.2.1 on Windows 10 and I use the input code below. Does anyone know how I can use all 32? Thank you!</p> <p>INPUT:</p> <pre><code>! B3LYP 6-311++G** tightSCF NEB-TS FREQ %scf MaxIter 300000 end %pal nprocs 32 end %base &quot;set1&quot; %NEB NEB_END_XYZFILE &quot;set1_end.xyz&quot; END </code></pre> https://mattermodeling.stackexchange.com/q/7163 4 Simple code for polarizable force-field molecular dynamics? Wesley https://mattermodeling.stackexchange.com/users/3606 2021-11-29T00:23:35Z 2021-11-29T00:30:50Z <p>I am interested in writing my own molecular dynamics code that uses a polarizable force-field. I am wondering if there are relatively simple &quot;toy repositories&quot; for these models such as is very common for pairwise FF's. The <a href="https://github.com/Allen-Tildesley/examples/tree/master/python_examples" rel="nofollow noreferrer">Allen-Tildesly</a> python/fortran GIT repo is an excellent example for pair-wise additive models.</p> <p>There are three types of polarizable force-fields that meet the criteria that I am after:</p> <ol> <li>atomic multipoles</li> <li>drude oscillators</li> <li>fluctuating charge models.</li> </ol> <p>What these have in common is an underlying pairwise additive force-field that in addition accounts for the many body contribution from polarizability.</p> <p>This is all under the molecular mechanics umbrella, not ab-initio or more rigorous. A well written code should be able to sample in the nano-seconds per day for thousands of molecules, on 12 or less cpus, with the type of polarizable model I am after.</p> https://mattermodeling.stackexchange.com/q/7162 6 How to numerically calculate quantum state distance using quantum metric? TribalChief https://mattermodeling.stackexchange.com/users/1766 2021-11-28T23:06:49Z 2021-11-29T05:18:41Z <p>In <a href="https://arxiv.org/abs/1012.1337" rel="nofollow noreferrer">Ran Cheng's review of the quantum geometric tensor</a>, eq. (11) gives the tensor as: <span class="math-container">$$Q_{\mu\nu}=\sum_{n\neq 0}\frac{\langle\phi_0|\partial_\mu H|\phi_n\rangle\langle\phi_n|\partial_\nu H|\phi_0\rangle}{(E_0-E_n)^2}.$$</span> Per eq. (6), we see that the quantum metric may be defined as: <span class="math-container">$$g_{\mu\nu}=\text{Re }Q_{\mu\nu}.$$</span> I now want to calculate the distance between two arbitrary quantum states of a two-level system parameterized by two variables <span class="math-container">$(k_x,k_y)$</span> using eq. (9): <span class="math-container">$$|\langle\phi(\lambda_F)|\phi(\lambda_I)\rangle|=1-\frac{1}{2}\int_{\lambda_I}^{\lambda_F} g_{\mu\nu}(\lambda)d\lambda^\mu d\lambda^\nu.$$</span></p> <p>Could someone verify that the steps I'm taking are correct? The results of my numerical simulations seem suspicious.</p> <ol> <li>Find the two eigenvectors of the 2-level Hamiltonian (not resulting in the nice standard eigenvectors discussed in Cheng's work).</li> <li>Use these to calculate <span class="math-container">$g_{k_x k_x},g_{k_x k_y},g_{k_y k_x}$</span> and <span class="math-container">$g_{k_y k_y}$</span>.</li> <li>To perform the path integral, I first parameterize some path in <span class="math-container">$k$</span>-space (for example using <span class="math-container">$k_x (t) = \sin(t), k_y(t) = \cos(t)$</span>).</li> <li>Plug these <span class="math-container">$k_x(t),k_y(t)$</span> into <span class="math-container">$g_{\mu\nu}$</span> found in step 2.</li> <li>Using motivation from eq. (21) of the review, numerically integrate the following, for absolute value of some <span class="math-container">$x$</span> indicated by <span class="math-container">$|x|$</span>: <span class="math-container">$$|\langle\phi(\lambda_F)|\phi(\lambda_I)\rangle|=1-\frac{1}{2}\int_{\lambda_I}^{\lambda_F} \sqrt{ \left|g_{k_x k_x} \left(\frac{dk_x}{dt}\right)^2\right|+ \left|g_{k_x k_y}\left(\frac{dk_x}{dt}\right)\left(\frac{dk_y}{dt}\right)\right|+ \left|g_{k_y k_x}\left(\frac{dk_y}{dt}\right)\left(\frac{dk_x}{dt}\right)\right|+ \left|g_{k_y k_y}\left(\frac{dk_y}{dt}\right)^2\right| } dt.$$</span> I am supposed to get an answer between <span class="math-container">$0$</span> and <span class="math-container">$1$</span>, but I am not sure I incorporated/defined the metric correctly. Any advice?</li> </ol> <hr /> <p>UPDATE: As requested, here is (Mathematica) code that I used:</p> <pre><code>(* Some Hamiltonian H[kx,ky] with eigenvectors |n[kx,ky]&gt;,|p[kx,ky]&gt; \ and eigenvalues Energy[kx,ky]*) m = 0.1; sx = {{0, 1}, {1, 0}}; sy = {{0, -I}, {I, 0}}; sz = {{1, 0}, {0, -1}}; H[kx_, ky_] = m sz + kx sz + ky sy; p[kx_, ky_] = Eigenvectors[H[kx, ky]][]/Norm[Eigenvectors[H[kx, ky]][]]; n[kx_, ky_] = Eigenvectors[H[kx, ky]][]/Norm[Eigenvectors[H[kx, ky]][]]; Energy[kx_, ky_] = Eigenvalues[H[kx, ky]]; (* Components of Quantum geometric tensor *) Qxx[kx_, ky_] = ((Conjugate[n[kx, ky]] . D[H[kx, ky], kx] . p[kx, ky]) (Conjugate[p[kx, ky]] . D[H[kx, ky], kx] . n[kx, ky]))/(Energy[kx, ky][] - Energy[kx, ky][])^2; Qxy[kx_, ky_] = ((Conjugate[n[kx, ky]] . D[H[kx, ky], kx] . p[kx, ky]) (Conjugate[p[kx, ky]] . D[H[kx, ky], ky] . n[kx, ky]))/(Energy[kx, ky][] - Energy[kx, ky][])^2; Qyx[kx_, ky_] = ((Conjugate[n[kx, ky]] . D[H[kx, ky], ky] . p[kx, ky]) (Conjugate[p[kx, ky]] . D[H[kx, ky], kx] . n[kx, ky]))/(Energy[kx, ky][] - Energy[kx, ky][])^2; Qyy[kx_, ky_] = ((Conjugate[n[kx, ky]] . D[H[kx, ky], ky] . p[kx, ky]) (Conjugate[p[kx, ky]] . D[H[kx, ky], ky] . n[kx, ky]))/(Energy[kx, ky][] - Energy[kx, ky][])^2; (* For integral, parameterize by g the k-space path (qx[g],qy[g]) of \ radius r, center (kx0,ky0). *) r = 1; kx0 = 0; ky0 = 0; qx[g_] = kx0 + r Cos[g]; qy[g_] = ky0 + r Sin[g]; (* Derivatives of qx[g],qy[g] for integral metric*) dqx[g_] = D[qx[g], g]; dqy[g_] = D[qy[g], g]; (* Components of metric tensor*) gxx[kx_, ky_] = Re[Qxx[kx, ky]]; gxy[kx_, ky_] = Re[Qxy[kx, ky]]; gyx[kx_, ky_] = Re[Qyx[kx, ky]]; gyy[kx_, ky_] = Re[Qyy[kx, ky]]; (* Starting and ending points of g, for integration limits. If \ gend=2Pi, I expect the distance to = 0, since they are the same point \ as the parameterized path is then that of a closed circle. *) gstart = 0; gend = 3/4 Pi; (* Quantum distance: I am not sure whether my definition of the \ metric is correct. *) distance = 1 - (1/2) NIntegrate[ Sqrt[Abs[gxx[qx[g], qy[g]] dqx[g] dqx[g]] + Abs[gxy[qx[g], qy[g]] dqx[g] dqy[g]] + Abs[gyx[qx[g], qy[g]] dqy[g] dqx[g]] + Abs[gyy[qx[g], qy[g]] dqy[g] dqy[g]]], {g, gstart, gend}] </code></pre> https://mattermodeling.stackexchange.com/q/7161 8 Study of supercell after creating vacuum poonam sharma https://mattermodeling.stackexchange.com/users/4354 2021-11-28T17:48:43Z 2021-11-29T15:25:09Z <p>For studying a bulk supercell, after creating some vacuum in it, I'm confused about how to relax it.</p> <p>With VASP, I can do relaxation using <code>NSW = 0</code> and <code>ISIF</code> tag 2 or 3. Alternatively, I could set <code>NSW=100</code> and with some value for <code>ISIF</code> (not sure what would be best).</p> <p>A third option is to first relax the supercell, then after creating a vacuum, it is should be fine to select <code>ISIF=0</code> for relaxation.</p> <p>I am not sure which one of these is the best option or whether there is a better alternative.</p> https://mattermodeling.stackexchange.com/q/7156 6 Relation between lattice parameter and energy for relaxations Maulesh VALA https://mattermodeling.stackexchange.com/users/4238 2021-11-28T05:42:12Z 2021-11-30T15:24:32Z <p>We have been wanting to do relaxation of lattice parameters as a function of the energy. I want to know the mathematical expression for this, and also the theoretical background related to this method. Thank you in advance.</p> https://mattermodeling.stackexchange.com/q/7155 8 what do I need to change about typical VASP input file to calculate the energy of a single atom? poonam sharma https://mattermodeling.stackexchange.com/users/4354 2021-11-27T23:20:56Z 2021-11-28T14:49:37Z <p>I'm a little confused how to make a VASP input file to calculate the energy for the isolated atom:</p> <ol> <li><p>Do I need to change the lattice parameter of my unit cell or can keep the value for the whole system?</p> </li> <li><p>If I have 4 atoms of one type in my unit cell, can I consider the position of any of them or must it be in the middle of the unit cell?</p> </li> <li><p>I observed that some people use K point set <span class="math-container">$1\times1\times1$</span> for calculating a single atom. Is it necessary to use this set or can I use the normal K points set that is used at the time of convergence?</p> </li> </ol> <p>To boil it down to one question, <strong>what do I need to change about typical VASP input file to calculate the energy of a single atom?</strong></p> https://mattermodeling.stackexchange.com/q/7153 5 VASP Memory Estimate Tristan Maxson https://mattermodeling.stackexchange.com/users/697 2021-11-27T19:35:31Z 2021-11-27T19:35:31Z <p>Is there any way to get a memory estimate for VASP calculations either directly or indirectly (based on some example calculation)? For example, I would like to be able to predict based on my settings how much memory is needed within about a GB per core.</p> https://mattermodeling.stackexchange.com/q/7151 7 Suggestions on laptops for matter modeling EverydayFoolish https://mattermodeling.stackexchange.com/users/784 2021-11-27T17:12:36Z 2021-11-29T18:47:32Z <p>While there's a lot of good information available out there about choosing laptops, I still find it hard to pick a personal machine for my scientific computing needs. Though most matter modelling researchers, run the bulk of their calculations on computing clusters, the need for a powerful personal computing machine still seems unavoidable. For a few reasons like:</p> <ul> <li>Run some back-of-the-envelope-style quick numerics/computations</li> <li>Post-simulation analysis with scripting tools</li> <li>Plotting, Creating illustrations (for example with Blender or something similar) etc.</li> <li>Code Development (especially for people contributing to various packages across the board)</li> </ul> <p>A few parameters to consider in this context:</p> <p><strong>Processors</strong></p> <ul> <li>Intel (usually seemed to be the preferred ones due to Intel MKl and oneAPI)</li> <li>AMD (though not the default choice, they seem to be getting better)</li> <li>Apple silicon (They seem promising, but I am not sure if people in the community are already adopting these new architectures)</li> </ul> <p><strong>Other relevant Hardware specs</strong></p> <ul> <li>RAM</li> <li>SSDs</li> <li>integrated GPUs</li> </ul> <p>What kind of laptops would you recommend for scientific computing keeping the above parameters in mind?</p> https://mattermodeling.stackexchange.com/q/7150 6 How reactivity of a organic molecule depends upon HOMO and LUMO astha https://mattermodeling.stackexchange.com/users/789 2021-11-27T14:37:44Z 2021-11-27T19:37:17Z <p>I am studying the dehydrogenation of an organic molecule. I see the HUMO-LUMO gap remains nearly the same for many dehydrogenated steps (for some steps, it is exactly the same) while the position of HOMO and LUMO has shifted slightly. So, for the steps, I have a gap between, HOMO and LUMO same, I need to consider the position of the HOMO and LUMO to explain my dehydrogenation steps.</p> <p>Here are my data.</p> <p>Could you please suggest how HOMO and LUMO affect the reactivity of the molecule? Also, which edge (HOMO or LUMO) is more responsible for the reactivity of the molecule?</p> <p><a href="https://i.stack.imgur.com/Cmdx5.png" rel="noreferrer"><img src="https://i.stack.imgur.com/Cmdx5.png" alt="enter image description here" /></a></p> https://mattermodeling.stackexchange.com/q/7149 5 How to plot berry curvature flux by considering plane in momentum space? UJM https://mattermodeling.stackexchange.com/users/1361 2021-11-27T12:42:34Z 2021-11-27T12:42:34Z <p>I want to plot the berry curvature flux by considering <span class="math-container">$k_x$</span> and <span class="math-container">$k_y$</span> plane in momentum space. I have experience running DFT calculations in Quantum ESPRESSO. I have tried reading the user manual of Wannier90 tool but didn't find any way to do this. The below image can be referred for more understanding of what I am trying to do: <a href="https://i.stack.imgur.com/ptZjG.png" rel="noreferrer"><img src="https://i.stack.imgur.com/ptZjG.png" alt="enter image description here" /></a></p> <p>I am not asking for actual code but just the steps which I have to follow in Wannier90 to achieve this results. Any help will be appreciable regarding this!<br /> Thank you!</p> https://mattermodeling.stackexchange.com/q/7146 6 Installing Quantum Espresso on an Apple M1 processor possible? Paul Eugenio https://mattermodeling.stackexchange.com/users/4543 2021-11-26T17:00:48Z 2021-11-30T01:44:00Z <p>I'm attempting to make QEspresso's pw program on a new 2021 MacBook Air, which has an M1 processor. While ./configure does not throw any errors, running 'make pw' fails with the following output:</p> <pre><code>checking build system type... Invalid configuration aarch64-apple-darwin20.6.0': machine aarch64-apple' not recognized configure: error: /bin/sh ./config/config.sub aarch64-apple-darwin20.6.0 failed if test -d src/ ; then \ ( cd src/ ; make ) ; fi make: *** No rule to make target device_auxfunc_mod.o', needed by deviceXlib_mod.o'. Stop. make: *** [libsrc] Error 2 make: *** [libcuda_devxlib] Error 2 make: *** [libcuda] Error 2 </code></pre> <p>I included what I believe are the relevant lines of the make output. The output prior to this seemed normal. I believe CUDA is related to parallelization, which I don't need right now, so I tried disabling parallelization as a make option -- yet this does not work. I've also tried</p> <pre><code>sudo ./configure --disable-parallel --with-internal-FFTW --with-internal-blas --with-internal-lapack ARCH=&quot;mac686&quot; </code></pre> <p>following the instructions of Ref  for Macs, however, I don't know if I need to manual set ARCH=&quot;mac686&quot;, or something different for the newer M1. Or maybe this is entirely the wrong direction.</p> <p>Has anyone tried installing QEspresso on an M1 Mac yet? Or have any sense if this is currently even possible? My web search only dug up one reference to installing QEspresso on the new M1 (see Ref ), which was totally unhelpful, so I'm afraid I'm running into a dead end and major time sink.</p> <p>Ref : <a href="https://sites.google.com/a/ncsu.edu/cjobrien/tutorials-and-guides/pwscf" rel="noreferrer">https://sites.google.com/a/ncsu.edu/cjobrien/tutorials-and-guides/pwscf</a></p> <p>Ref : <a href="https://lists.quantum-espresso.org/pipermail/developers/2021-July/002430.html" rel="noreferrer">https://lists.quantum-espresso.org/pipermail/developers/2021-July/002430.html</a></p> https://mattermodeling.stackexchange.com/q/7125 7 Building model of Graphene Oxide Roshan Shrestha https://mattermodeling.stackexchange.com/users/1791 2021-11-23T08:53:01Z 2021-11-30T01:16:25Z <p>I used to build some small molecules using Avogadro. Now, I want to build a large molecule, Graphene oxide which unfortunately doesn't have a definite structure with different levels of oxidation. Can someone please suggest me how can we build such single sheet/layer of Graphene Oxide (GO) on Avogadro or any other tools? I will be extremely grateful for any inputs/suggestions.</p> https://mattermodeling.stackexchange.com/q/7120 10 Qualitatively, How do MEAM Potentials Work? Connor https://mattermodeling.stackexchange.com/users/4220 2021-11-22T15:47:09Z 2021-11-29T15:50:43Z <p>I have frequently come across MEAM potentials in my work, but I lack an intuitive understanding of what they do.</p> <p>What's a good qualitative description of a MEAM potential function?</p> https://mattermodeling.stackexchange.com/q/7058 9 What software can I use for gas adsorption calculations? PBH https://mattermodeling.stackexchange.com/users/4232 2021-11-15T15:43:39Z 2021-11-29T01:35:27Z <p>We are from a new research group working on matter modelling. Currently our work has focused mainly on classical Molecular Dynamics (MD), Lattice Dynamics (LD) and ab-initio methods. For these, we have been using <a href="https://www.lammps.org/" rel="noreferrer">LAMMPS</a>, <a href="http://gulp.curtin.edu.au/gulp/" rel="noreferrer">Gulp</a>, <a href="https://departments.icmab.es/leem/siesta/Documentation/index.html" rel="noreferrer">SIESTA</a>, <a href="https://www.quantum-espresso.org/" rel="noreferrer">Quantum Espresso</a> and <a href="https://www.cp2k.org/" rel="noreferrer">CP2K</a>.</p> <p>Although we are currently studying the thermoelectric properties of semiconductor materials, we would like to expand our research focus to other areas <strong>such as gas adsorption as well</strong>.</p> <p><em><strong>What software can we use for gas adsorption?</strong></em> I am particularly interested in the ability to simulate larger system sizes, acceleration methods, interoperability with other third party tools, ease of use, etc. We are looking at both commercial as well as free packages.</p> <p>Thanks</p> https://mattermodeling.stackexchange.com/q/6889 14 Looking for crystal generator library alfC https://mattermodeling.stackexchange.com/users/4417 2021-10-13T23:46:31Z 2021-11-30T09:43:52Z <p>I am looking for a C or a C++ library that can do crystal generation, that is, multiply unit cells in one or more directions with symmetry information. (in other words, generate supercells). I have been using OpenBabel (also C++) but it doesn't have this function (it is more oriented to molecules).</p> <p>If the library can read or write CIF or other similar formats that would be even better.</p> <p>Can you recommend one?</p> <p>I know that libraries like this exist in Python, e.g. ASE, but I need to generate them on the fly (e.g from CIF files.)</p> <p>I am not looking in particular to generate random periodic structures, but it is fine as long as the simpler case I mention above can be performed as well.</p> https://mattermodeling.stackexchange.com/q/6853 6 How Do you Produce your own MEAM Potentials? Connor https://mattermodeling.stackexchange.com/users/4220 2021-10-06T15:21:56Z 2021-11-29T19:09:47Z <p>I have come across the <a href="https://icme.hpc.msstate.edu/mediawiki/index.php/MPC.html" rel="nofollow noreferrer">MEAM Parameter Calibration toolkit</a> (link leads to Wiki, video tutorials, and download link for the package) for fitting your own MEAM potentials .</p> <p>Is this the best software out there for the job? Or is there another way of creating/ fitting your own MEAM potentials?</p> <ol> <li>Barrett, C.D., Carino, R.L. The MEAM parameter calibration tool: an explicit methodology for hierarchical bridging between ab initio and atomistic scales. Integr Mater Manuf Innov 5, 177–191 (2016). <a href="https://doi.org/10.1186/s40192-016-0051-6" rel="nofollow noreferrer">DOI</a></li> </ol> https://mattermodeling.stackexchange.com/q/6269 7 Error when using pycotem to index an electron diffraction pattern? user3679 https://mattermodeling.stackexchange.com/users/3679 2021-06-29T00:35:35Z 2021-11-29T19:16:11Z <p>In the <a href="https://github.com/mompiou/pycotem" rel="nofollow noreferrer">pycotem code</a>, this error comes up when using the Diffraction GUI.</p> <pre><code>pycotem\diffraction_main_.py&quot;, line 186, in angle_check inc = ui.ListBox_d_2.currentItem().text().split(',') AttributeError: 'NoneType' object has no attribute 'text' </code></pre> <p>Has anyone tried to resolve this?</p> https://mattermodeling.stackexchange.com/q/4828 8 How to go from tinker parameters to a GROMACS itp file, specifically for dihedrals? [closed] megamence https://mattermodeling.stackexchange.com/users/1169 2021-04-26T19:10:19Z 2021-11-29T21:00:31Z <p>I am trying to write an itp file for the compound 1,2-diethoxyethance (CCOCCOCC).I used tinker analyze to obtain the parameter file, f2.out, which I have attached to this post. In order to check if my procedure was right, I downloaded an itp file from LigParGen (UNL_6B2B1D.itp).</p> <p>Every parameter in my topology file (topol.itp) matched with the parameters from LigParGen, except the dihedrals with hydrogen.</p> <p>The formulae I used to go from the Torsional Angle Parameters in tinker were the ones given in the GROMACS page: <a href="https://manual.gromacs.org/documentation/2020-beta3/reference-manual/functions/bonded-interactions.html" rel="nofollow noreferrer">https://manual.gromacs.org/documentation/2020-beta3/reference-manual/functions/bonded-interactions.html</a>, equation block 33.</p> <p>If I look at the torsional angle parameters for torsion #11 in f2.out:</p> <p>7 2 6 9 -0.521 0/1 -2.018 180/2 1.996 0/3</p> <p>So, <span class="math-container">$F_1 = -0.521, F_2 = -2.018, F_3 = 1.996, F_4 = 0$</span></p> <p>I use the GROMACS formula: <span class="math-container">$$c_0 = (F_2+(F_1+F_3)/2)\times4.184 = -5.358\\ c_1 = 0.5\times(-F_1+3F_3)\times 4.184 = 13.617\\ c_2 = (-F_2 + 4F_4)\times 4.184 = 8.443\\ c_3 = -2F_3\times4.184 = -16.7025\\ c_4 = -4F_4 = 0\\ c_5 = 0\\$$</span> However, I look at the UNL file, I see that:</p> <p>7 2 6 9 3 1.590 4.770 0.000 -6.360 -0.000 0.000</p> <p>Clearly, the <span class="math-container">$c_i$</span> don't match. Why is this the case? Where am I going wrong? Every other torsion matches the formula given in block 33 of the gromacs manual page. I would appreciate any advice you have.</p> <p>Some relevant lines from f2.out (I have added ## to show the lines I have used above):</p> <pre><code>Torsional Angle Parameters : Atom Numbers Amplitude, Phase and Periodicity 1 3 1 2 6 0.468 0/3 2 3 1 2 7 0.300 0/3 3 3 1 2 8 0.300 0/3 4 4 1 2 6 0.468 0/3 5 4 1 2 7 0.300 0/3 6 4 1 2 8 0.300 0/3 7 5 1 2 6 0.468 0/3 8 5 1 2 7 0.300 0/3 9 5 1 2 8 0.300 0/3 10 1 2 6 9 0.650 0/1 -0.250 180/2 0.670 0/3 11 7 2 6 9 -0.521 0/1 -2.018 180/2 1.996 0/3 ## 12 8 2 6 9 -0.521 0/1 -2.018 180/2 1.996 0/3 13 2 6 9 10 0.650 0/1 -0.250 180/2 0.670 0/3 14 2 6 9 11 -0.521 0/1 -2.018 180/2 1.996 0/3 15 2 6 9 12 -0.521 0/1 -2.018 180/2 1.996 0/3 16 6 9 10 13 -0.550 0/1 17 6 9 10 14 0.468 0/3 18 6 9 10 15 0.468 0/3 19 11 9 10 13 0.468 0/3 20 11 9 10 14 0.300 0/3 21 11 9 10 15 0.300 0/3 22 12 9 10 13 0.468 0/3 23 12 9 10 14 0.300 0/3 24 12 9 10 15 0.300 0/3 25 9 10 13 16 0.650 0/1 -0.250 180/2 0.670 0/3 26 14 10 13 16 -0.521 0/1 -2.018 180/2 1.996 0/3 27 15 10 13 16 -0.521 0/1 -2.018 180/2 1.996 0/3 28 10 13 16 17 0.650 0/1 -0.250 180/2 0.670 0/3 29 10 13 16 18 -0.521 0/1 -2.018 180/2 1.996 0/3 30 10 13 16 19 -0.521 0/1 -2.018 180/2 1.996 0/3 31 13 16 17 20 0.468 0/3 32 13 16 17 21 0.468 0/3 33 13 16 17 22 0.468 0/3 34 18 16 17 20 0.300 0/3 35 18 16 17 21 0.300 0/3 36 18 16 17 22 0.300 0/3 37 19 16 17 20 0.300 0/3 38 19 16 17 21 0.300 0/3 39 19 16 17 22 0.300 0/3 </code></pre> <p>Relvant lines from UNL_6B2B1D.itp (have added semicolons to denote the line I have mentioned above:</p> <pre><code>[ dihedrals ] ; PROPER DIHEDRAL ANGLES ; ai aj ak al funct c0 c1 c2 c3 c4 c5 10 9 6 2 3 1.715 2.845 1.046 -5.607 -0.000 0.000 17 16 13 10 3 1.715 2.845 1.046 -5.607 -0.000 0.000 9 6 2 1 3 1.715 2.845 1.046 -5.607 -0.000 0.000 16 13 10 9 3 1.715 2.845 1.046 -5.607 -0.000 0.000 9 6 2 8 3 1.590 4.770 0.000 -6.360 -0.000 0.000 16 13 10 15 3 1.590 4.770 0.000 -6.360 -0.000 0.000 9 6 2 7 3 1.590 4.770 0.000 -6.360 -0.000 0.000 ;;;;; 16 13 10 14 3 1.590 4.770 0.000 -6.360 -0.000 0.000 8 2 1 4 3 0.628 1.883 0.000 -2.510 -0.000 0.000 15 10 9 12 3 0.628 1.883 0.000 -2.510 -0.000 0.000 7 2 1 3 3 0.628 1.883 0.000 -2.510 -0.000 0.000 7 2 1 4 3 0.628 1.883 0.000 -2.510 -0.000 0.000 20 17 16 19 3 0.628 1.883 0.000 -2.510 -0.000 0.000 7 2 1 5 3 0.628 1.883 0.000 -2.510 -0.000 0.000 15 10 9 11 3 0.628 1.883 0.000 -2.510 -0.000 0.000 14 10 9 12 3 0.628 1.883 0.000 -2.510 -0.000 0.000 8 2 1 3 3 0.628 1.883 0.000 -2.510 -0.000 0.000 8 2 1 5 3 0.628 1.883 0.000 -2.510 -0.000 0.000 21 17 16 19 3 0.628 1.883 0.000 -2.510 -0.000 0.000 22 17 16 18 3 0.628 1.883 0.000 -2.510 -0.000 0.000 21 17 16 18 3 0.628 1.883 0.000 -2.510 -0.000 0.000 14 10 9 11 3 0.628 1.883 0.000 -2.510 -0.000 0.000 20 17 16 18 3 0.628 1.883 0.000 -2.510 -0.000 0.000 22 17 16 19 3 0.628 1.883 0.000 -2.510 -0.000 0.000 21 17 16 13 3 0.979 2.937 0.000 -3.916 -0.000 0.000 15 10 9 6 3 0.979 2.937 0.000 -3.916 -0.000 0.000 22 17 16 13 3 0.979 2.937 0.000 -3.916 -0.000 0.000 20 17 16 13 3 0.979 2.937 0.000 -3.916 -0.000 0.000 14 10 9 6 3 0.979 2.937 0.000 -3.916 -0.000 0.000 18 16 13 10 3 1.590 4.770 0.000 -6.360 -0.000 0.000 19 16 13 10 3 1.590 4.770 0.000 -6.360 -0.000 0.000 12 9 6 2 3 1.590 4.770 0.000 -6.360 -0.000 0.000 11 9 6 2 3 1.590 4.770 0.000 -6.360 -0.000 0.000 6 2 1 5 3 0.979 2.937 0.000 -3.916 -0.000 0.000 13 10 9 12 3 0.979 2.937 0.000 -3.916 -0.000 0.000 6 2 1 4 3 0.979 2.937 0.000 -3.916 -0.000 0.000 6 2 1 3 3 0.979 2.937 0.000 -3.916 -0.000 0.000 13 10 9 11 3 0.979 2.937 0.000 -3.916 -0.000 0.000 13 10 9 6 3 -1.151 1.151 0.000 -0.000 -0.000 0.000 <span class="math-container">`</span> </code></pre> https://mattermodeling.stackexchange.com/q/4678 7 Example of a standard/archetypal/simple 4-band gapped condensed matter model with analytic results? TribalChief https://mattermodeling.stackexchange.com/users/1766 2021-04-08T02:38:59Z 2021-11-30T20:54:22Z <p>I am looking to study Berry phase-like phenomena in a <strong>gapped</strong> 4-band material model. In particular, I want to numerically and analytically calculate the Abelian Berry curvature integral of each band over some region of k-space. It should be easy to calculate the Chern number of this system.</p> <p>However, I am having trouble finding a widely-used 4-band model with analytic expressions for wavefunctions and energies. I am looking to compare results from numerical methods vs analytical ones; and would ideally already have these models in terms of k-space variables in some reasonable basis. <strong>Ultimately, I want to toy with this model by changing its diagonal values to see how bands 'invert' after a gap-closing, and how their Berry curvatures change accordingly. Ideally, it would be easy to see edge states in a domain-wall-like setup, due to varying of an x-dependent diagonal/potential factor.</strong></p> <p>I first tried the BHZ model for the Z2 invariant (as recommended by the answer to this poorly-asked previous attempt of this question <a href="https://mattermodeling.stackexchange.com/questions/4673/example-of-an-standard-archetypal-simple-4-band-un-gapped-condensed-matter-model">here</a>). However, the band degeneracies make it hard to study what I want to study: the Abelian Berry curvature is not well-defined; and when I tune the diagonal with some constant to force it to &quot;gap&quot;, the band crossings are too complicated. For example, the gap can close at several points besides the Gamma point.</p> <p>The closest I got was some effective Hamiltonians for bilayer graphene in <a href="https://arxiv.org/pdf/1205.6953.pdf" rel="nofollow noreferrer">this PDF</a> (such as equation 76). However, solving for wavefunctions took a while using Mathematica, and led to messy-looking algebraic expressions. Isn't there a simpler model out there, of theoretical value? Or just a model that justifies using not-so-simple expressions? I would find any appropriate 4-band condensed matter models very useful! Even suggestions for a simple/absurd toy model with potential nontrivial topology are welcome. Thank you!</p> https://mattermodeling.stackexchange.com/q/1921 22 What are the tools available for point defects calculations? Franksays https://mattermodeling.stackexchange.com/users/1031 2020-08-05T06:12:52Z 2021-11-30T20:29:33Z <p>It would be appreciated if you could explain one of the tools below (or another tool not listed), in the format used here (for example):</p> <ul> <li><a href="https://mattermodeling.stackexchange.com/q/4501/5">What software will allow me to combine two images?</a></li> <li><a href="https://mattermodeling.stackexchange.com/a/1222/5">What software is available to do molecular dynamics on Windows?</a></li> <li><a href="https://mattermodeling.stackexchange.com/q/414/5">Is there a free package with robust CASSCF functionality?</a></li> </ul> <p><strong>One software description per answer please.</strong></p> <ul> <li>PyCDT</li> <li>PyDEF</li> <li>pylada</li> <li>pymatgen (the parts for point defect calculations)</li> </ul> https://mattermodeling.stackexchange.com/q/1739 9 How does infinite DMRG work? taciteloquence https://mattermodeling.stackexchange.com/users/97 2020-07-27T08:58:20Z 2021-11-30T20:34:00Z <p>iDMRG or infinite-size density matrix renormalization group, is a common technique in condensed matter. It seems that usually people believe that it reliably captures infinite-size behavior. I have found plenty of resources describing <strong>how</strong> it works (mathematically), but I want a <strong>heuristic/intuitive explanation</strong> for how a system composed of effectively two sites (each with a large tensor) can capture physics that is occurring at all different length scales.</p> https://mattermodeling.stackexchange.com/q/1733 14 Why does the Wolff algorithm slow down in a 4-body Ising model? Jun_Gitef17 https://mattermodeling.stackexchange.com/users/379 2020-07-27T05:07:30Z 2021-11-30T20:40:35Z <p>In the <a href="https://journals.aps.org/prb/abstract/10.1103/PhysRevB.95.041101" rel="nofollow noreferrer">paper</a> that introduced &quot;Self-learning MC&quot; (an ML-inspired MC technique, as I understand) the authors consider a many-body Ising model as an example to show the efficiency of their algorithm. The model looks like this: <span class="math-container">\begin{equation} H= -J \sum_{\langle i,j\rangle} S_i S_j - K \sum_{ijkl\in p}S_iS_jS_k S_l \tag{1} , \end{equation}</span> where the second term runs for all plaquettes <span class="math-container">$p$</span> on the square lattice.</p> <p>In the paper, I found an explanation that says <em>&quot;For <span class="math-container">$K=0$</span>, this model reduces to the standard Ising model which can be simulated efficiently by the Wolff method. However, for <span class="math-container">$K\neq0$</span>, no simple and efficient global update method is known.&quot;</em> The Wolff algorithm <strong>can</strong> be applied to this model, and they indeed compare the &quot;naive Wolff algorithm&quot; with the new self-learning MC. It seems that while the Wolff algorithm does speed up MC compared to local updates, it still has a very similar asymptotic suffering in relaxation (Fig 3 in the paper).</p> <p>My question is this: Is there an intuitive way to understand <em><strong>why</strong></em> this slowing down happens in the Wolff algorithm? To me, it seems like it might work just fine as in the 2-body Ising model, because it's not that different (at least in terms of implementation).</p> https://mattermodeling.stackexchange.com/q/1678 11 How to choose the values of J and spin parameters in a heterogeneous spin system? Camps https://mattermodeling.stackexchange.com/users/24 2020-07-25T17:41:11Z 2021-11-30T20:42:07Z <p>In this <a href="https://doi.org/10.1016/j.jmmm.2017.01.004" rel="nofollow noreferrer">work</a>, graphene-based systems that are described by mixed spin-3/2 and spin-5/2 are studied using the <a href="/questions/tagged/ising-model" class="post-tag" title="show questions tagged &#39;ising-model&#39;" rel="tag">ising-model</a>. A diagram of the structure is shown bellow:</p> <p><a href="https://i.stack.imgur.com/VMBeV.png" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/VMBeV.png" alt="enter image description here" /></a></p> <p>The Hamiltonian used is:</p> <p><span class="math-container">\begin{equation} \tag{1} {\small {H_I} = - J\sum\limits_{\left\langle {i,j} \right\rangle } {{S_i}{\sigma _j}} - {J_\sigma }\sum\limits_{\left\langle {i,j} \right\rangle } {{\sigma _i}{\sigma _j}} - {J_S}\sum\limits_{\left\langle {i,j} \right\rangle } {{S_i}{S_j}} - {K_v}\left( {\sum\limits_i {S_i^2} + \sum\limits_j {\sigma _j^2} } \right). } \end{equation}</span></p> <p>Here <span class="math-container">$\left\langle {i,j} \right\rangle$</span> refers to the sum over the nearest neighbors pairs, <span class="math-container">$\left[ i,j \right]$</span> means sum over the next-nearest neighbors pairs, <span class="math-container">$J$</span>, <span class="math-container">$J_\sigma$</span> and <span class="math-container">$J_S$</span> are the exchange interaction constants between sites <span class="math-container">$\sigma−S$</span>, <span class="math-container">$\sigma−\sigma$</span> and <span class="math-container">$S−S$</span>, respectively (see diagram above), and <span class="math-container">$K_v$</span> is the crystal field anisotropy constant. The spins moments can take values <span class="math-container">$\sigma = ±3/2,±1/2$</span> and <span class="math-container">$S=±5/2,±3/2,±1/2$</span>.</p> <h3>How are <span class="math-container">$J$</span>, <span class="math-container">$J_\sigma$</span>, <span class="math-container">$J_S$</span>, <span class="math-container">$\sigma$</span> and <span class="math-container">$S$</span> chosen?</h3> https://mattermodeling.stackexchange.com/q/110 29 What is Materials Modeling? Seaver https://mattermodeling.stackexchange.com/users/209 2020-04-30T19:08:27Z 2021-11-30T22:00:13Z <p>I'm a noob with zero knowledge of the subject. Materials Modeling is so specialized that it's not even on Wikipedia yet. Help orient a newcomer. What do you use it for? Can you use it to model materials for a bulletproof t-shirt, a superior mask to protect against COVID-19, a flux capacitor?</p>