aa aat Abascal abc abf ABI abi abo Abramyan absTol Acc Accelerys Accelrys acceptor Acceptor acceptors accessor accomx accomy accomz accuracies ach ackland Ackland acks acolor acos Acta actinide activationfunctions acylindricity addforce Addington addtorque adf Adhikari adiam adim Adjiman adof adp Adri advect advection advects affine Afrasiabian Afshar agilio Agilio agni Agnolin ahi Ahrens Ai Aidan aij aimd aip airebo Aj ajaramil ajs akohlmey Aktulga al alabel alain Alain Alamos alat Albe alchemical AlCu Alderton Alejandre Aleksei alessandro Alessandro Alexey ali aliceblue Allera Allinger allocatable allocator allocators allosws AlO alo Alonso Alperen alphak alphashrink amap Amatrix AMD amino Amirjalayer Amit amu Amzallag analytical Anders Andric Andrienko Andzelm Ang anglegrad angletangrad angmom angmomx angmomy angmomz Angs anharmonic anharmonicity aniso anisotropic anisotropies anisotropy ansi antiferromagnetic antiquewhite Antisymmetrized antisymmetry anton Antonelli api apolar 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btype buckPlusAttr buf builtin Bulacu Bulatov Bureekaew burlywood Bussi Buturigakkwaishi Buyl bvec bvecx bvecy bvecz Bybee bz Cadarache cadetblue Cagin calc calibrationfunctions calibrationparameters calibre caltech Caltech Camilloni Camiloni Campana Cangi Cao Capolungo Caro cartesian Cas CasP Caswell Cates cauchy cauchystat Cavazzoni Cavium Cawkwell cbecker ccache ccachepiecewise ccl ccmake ccN ccNspecies CCu cd cdeam cdennist cdof ceil Ceil cekk centerline centro centroid Centroid centrosymmetry Cercignani cercignanilampis Cerda ceriotti Ceriotti Cerutti cfg CFG cfile CFL cgdna CGDNA cgmap cgs cgsdk CGSDK cgspica CGSPICA Chaimovich Chalopin Champaign charmm CHARMM charmmfsh charmmfsw charptr Chaudhuri checkbox checkmark checkqeq checksum chemflag chemistries Chemnitz Cheng Chenoweth chiral chiralIDs ChiralIDs chirality Cho Chodera Choi ChooseOffset chris Christoph Chu chunkID chunksize Ciccotti Cieplak Cii Cij cis civ CKD ckk Clang clearstore Cleary Clebsch clemson Clermont clo 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cuFFT CuH Cui Cummins Cundall cundall Curk curv Cusentino customIDs cutbond cutghost cuthi cutinner cutlo cutmax cutoffA cutoffC cutsq cuu cv Cv Cval cvar cvec cvecx cvecy cvecz cvff cwiggle cx cy cygwin Cygwin cylindrically Cyrot cyrstals cython cz Daivis Dammak dampflag Darden darkblue darkcyan darkgoldenrod darkgray darkgreen darkkhaki darkmagenta darkolivegreen darkorange darkorchid darkred darksalmon darkseagreen darkslateblue darkslategray darkturquoise darkviolet Das Dasgupta dashpot dat datafile datatype datums Davidchack Daw dcd dcub Dcut de dE De deallocate deallocated debye Debye Decius decompositions decorrelation decrementing deeppink deepskyblue defgrad defn deformable Deissenbeck del delaystep deleteIDs DeleteIDs delflag Dellago delocalization delocalized Delong delr deltaHf deltamu dem Dendrimer dendritic Denniston Denoual dephase dephasing dequidt Dequidt der dereference dereferenced derekt Deresiewicz Derjagin Derjaguin Derlet Desbiens Deserno Destree destructor destructors detils Devanathan devel Devemy deviatoric Devine dewald df dfftw DFT dftb dh dhex di dia diag diagonalization diagonalize diagonalized diagonalizers diagonalizing Diallo diblock dichalcogenides Dickel diel Dietz differentiable diffusively diffusivities diffusivity dihedral dihedrals Dihedrals dihydride Dij dimdim dimensionality dimensioned dimgray dipolar dipoleflag dir Direc dirname discoverable discretization discretized discretizing disp dispersionflag dissipative Dissipative distharm distutils dl dlabel dlambda DLAMMPS dll dlm dlopen dm dmax Dmax dmg dmi dname dnf DNi Dobnikar Dobson docenv Dodds dodgerblue dof doi Donadio Donev dotc Doty downarrow doxygen doxygenclass doxygenfunction Doye Doyl dpd DPD dpdTheta dphi DPhil dpme dr dR dragforce Drautz dreiding Dreiding drfourth drho drsquared drude Drude DRUDE dsf dsmc dt dtemp dtgrow dtheta dtshrink dtype du dU Ducastelle Dudarev Dufils Duin Dullweber dumpfile Dunbrack Dunweg Dupend Dupont dUs Duval dV dvector dVx dW dx dy dylib dyn dyne dynes dynmat Dyre Dzyaloshinskii Eaa Eaat eam eangle earg eatom Eb Eba Ebeling ebend ebond ebook ebt ec Ec Echeverri eco ecoul ecp Ecut edgeIDs EdgeIDs edihed edim edip edn edpd eDPD edu ee Eebt ees eFF effm efield eflag eflux eg Eggebrecht ehex eHEX Ei eigen eigendecomposition eigensolve eigensolver eigensolvers eigenvalue eigenvalues eigenvector eigenvectors eij Eij Eijnden Eike eim eimp Eindhoven Eisenforschung Ejtehadi El el elaplong elastance Electroneg electronegative electronegativity electroneutral electroneutrality Eleftheriou ElementN elementset elementsets elif Elj Ellad ellipsoidflag elong Elsevier Elsner Elstner elt emacs emax Emax Embt emi Emmrich emol eN endian endocytosis energetics energyCorr eng Engility engilitycorp engrot engtrans engvib enobonds EnSight enthalpy enums envoke eos epair epcc epl Epp Epq eps Epton epub ePUB eq eqal eqch Eqp Eqq Eqs equi equidistance equil equilibrate equilibrated equilibrates equilibrating equilibration equilibria 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initializer initializations InitiatorIDs initio InP inq inregion instantiation Institut integrators Integrators intel intelmpi interal interatomic Interatomic interconvert interfacial interial interlayer intermolecular interoperable Interparticle interstitials intertube Intr intra intralayer intramolecular ints inumeric inv invariance invariants inversed invertible invertibility ionicities ionizable ionocovalent iOS iostreams iparam ipi ipp Ippolito IPv ipython IPython Isele isenthalpic ish Ishida iso isodemic isoenergetic isoenthalpic isokinetic isomorphism isothermal isotropically isovolume Isralewitz iter iteratively iters Ith Itsets itype itypeN iva Ivanov Ivector Iw Iwers iwyu ixcm ixhi ixlo ixx Ixx ixy Ixy ixz Ixz iy iycm iyy Iyy iyz Iyz iz izcm ized Izrailev Izumi Izvekov izz Izz Jacobian Jacobsen Jadhao Jadhav Jagielski jagreat Jahn Jalalvand james Janssen Janssens Jaramillo Jarzynski jatempl javascript jcp jea jec Jeffers jewett Jewett ji Jiang Jiao jik JIK jku jN Joannopoulos 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Martyna mary marys Masaglia Mashayak Massimilliano massless masstotal Masuhiro Matchett Materias mathbf mathjax matlab Matous matplotlib Matsubara Matteo Matteson Mattice Mattox Mattson maxangle maxbond maxchunk maxelt maxeval maxfiles Maxfoo maxima maxit maxiter maxsize maxspecial maxSteps maxstrain maxtry maxwell Maxwellian maxX Mayergoyz Mayoral mbt MBytes mc mcmoves McLachlan mcmoves md mdf mdi MDI mdpd mDPD mdtraj meam MEAM meamf meanDist mech Mechanobiology Mecke mediumaquamarine mediumblue mediumorchid mediumpurple mediumseagreen mediumslateblue mediumspringgreen mediumturquoise mediumvioletred Mees Mehl Mei Meissner Melchor Meloni Melrose mem Mem memalign MEMALIGN membered memcheck Mendelev Menon Menziani mer Meremianin Mersenne Merz meshless meso mesocnt mesodpd MESODPD mesont MESONT mesoparticle mesoscale mesoscopic metadata metadynamics Metadynamics metallicity Methfessel methine Metin meV Mezei mgpt MGPT mgptfast mh micelle micelles michael michele Mickel microcanonical microelastic microporous Microscale midnightblue mie Mie Mij Mikami Milano Militzer Minary mincap Mindlin mingw minhbonds minima minimizations minimizer minimizers minneigh minorder MinSizeRel minSteps mintcream Mintmire Miron mis misclassification Mises Mishin Mishra mistyped mistyrose Miyazaki Mj mK mkdir mkv mlength mliap mliappy mlparks Mniszewski mnt mobi Mobley modc Modell modelled modelling Modelling Modine moduli mofff MOFFF Mohd Mohles mol Mol molatom molfile Molfile molindex MolPairStyle moltemplate momb Monaghan Monaghans monodisperse monodispersity monolayer monopole monovalent Montalenti Monterey Montero Monti Monticelli Mora Morefoo Morfill Mori Moriya morris Morriss morse Morteza MoS Mosayebi Moseler Moskalev Moustafa mov mpi MPI mpicc mpiCC mpich mpicolor mpicxx mpiexec mpiio mpirun mplayer mpole mps mradius Mrovec Mryglod mscg MSCG msd msi MSI msm msmeam msmflag msse msst MtD Mth mtk Mtotal muB Muccioli mui Mukherjee Mulders Müller mult multi multibody Multibody 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nsq Nstart nstats Nstep Nsteps nsteps nsteplast Nstop nsub Nsw Nswap nt Nt Ntable ntheta nthreads ntimestep Ntptask Ntriples ntries ntris Ntype ntypes Ntypes nucleotide nucleotides nullptr num numa numactl numdiff numericalfreedom numerics numpy Numpy Nurdin Nvalue nvaluelast Nvalues nvar nvc nvcc nve nvidia nvk nvt Nwait NWChem nx Nx nxlo nxnodes Nxyz ny Ny nylo nz Nz nzlo ocl octahedral octants Ohara O'Hearn ohenrich ok Okabe Okamoto Okazaki O'Keefe OKeefe oldlace olecular Oleinik Olfason olivedrab Ollila Olvera omegaDD omegax omegay omegaz Omelyan omp OMP oneAPI onebody onelevel oneway onlysalt ons OO Oord opencl openKIM openmp OpenMP openmpi opls Oppelstrup optimizations orangered organometallic orientational orientationsFile orientorder originx originy originz Orlikowski ornl Ornstein Orsi ortho orthonormal orthorhombic Ortner os oso Otype Ouadfel Ouldridge outfile outmost outputss Ouyang overdamped overlayed Ovito oxdna oxDNA oxhi oxlo oxrna oxRNA packings padua Padua pafi PairIJ 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pylammps PyLammps pymbar pymodule pymol PySCF pythonic pytorch pyy Pyy pyz pz Pz pzz Pzz qbmsst qcore qdist qe qE qeff qelectron qeq QeQ QEq qfactor qfile qi Qi qj Qj Ql qm Qmin qmmm qmol qoffload qopenmp qoverride qqr qqrd Qsb qtb quadratically quadrupolar quadrupole quadrupoles Quant quartic quat quaternion quaternions quati quatj quatk quatw queryargs Queteschiner quickmin qw qx qy qz Rackers radi radialscreened radialscreenedspin radialspin radian radians radj Rafferty rahman Rahman Rajamanickam Ralf Raman ramped ramping Ramprasad Randisi randomizations rann RANN Rapetti Raphson Rappe Ravelo rc Rc Rci Rcm rcmax Rcmx Rcmy Rco Rcut rcut rcutfac rdc rdf RDideal rdx reacter Readline README real_t realtime realTypeMap reamin reax reaxff ReaxFF REAXFF rebo rebomos recurse recursing Ree refactored refactoring refactors reflectionstyle Reinders reinit reinitflag relaxbox relink relinked relres relTol relu RelWithDebInfo remappings remd Ren Rendon reneighbor reneighboring Reneighboring reneighborings Rensselaer reparameterizing repo representable reproducibility Reproducibility repuls reqid rescale rescaled rescales rescaling Rescaling respa RESPA respecified responder resquared REsquared restartfile restartinfo Restrepo rethrowing Revenga rewrap rezwanur rfac rfile rg Rg Rhaphson Rhe rheological rheology rhodo Rhodo rhodopsin rhok rhomax rhomin rhorho rhosum ri Ri Ribiere richard rigidID rigidify rij rIJ Rij RIj Rik Rin rin Rinaldi Rino RiRj Risi Rix Riy rj Rj Rjinner RjinnerN Rjk rjones Rjouter RjouterN rk rkf Rkinner RkinnerN Rkouter RkouterN rmask Rmask rmass rmax Rmax rmdir rmin Rmin RMS rmsd rnage rng rNEMD ro rocFFT Rochus Rockett rocksalt Rodrigues Rohart Ronchetti Ronevich Rosati Rosato Rosenberger Rossi Rossky rosybrown rotationally Rotenberg Rothenburg Rovigatti royalblue rozero Rperp Rr rRESPA Rsi Rso Rspace rsq rst rstyle Rubensson Rubia Rud Rudd Rudra Rudranarayan Rudzinski Runge runtime Rutuparna rx rxd rxnave rxnbond rxnsum ry Ryckaert Rycroft Rydbergs rz Rz Sabry saddlebrown Sadigh saed safezone Safran Sagui Saidi saip Salanne Salles sandia Sandia sandybrown sanitizer Sanyal Sanz Sarath sc scafacos SCAFACOS scalability scalable Scalable scalexy scalexz scaleyz Scalfi Schaik Scheid Schilfgarde Schimansky Schiotz Schlitter Schmid Schnieders Schoen Schotte Schratt Schulten Schunk Schuring Schwen Sci screenshot screenshots Scripps Scripta sd sdk sdpd SDPD se seagreen Searles Secor sectoring sed Seddon segmental Seifert Seleson sellerio Sellerio Semaev semiaxes semimetals Semin Sensable Seo Sep seqdep Serpico setfl setflag setforce Sethna setmask Setmask setpoint setvel sfftw sfree Sg sgcmc Shan Shanno Shapeev shapex shapey shapez shapshot shardlow Shardlow shawn Shen Shenderova Shi Shiga Shinoda Shiomi shlib shm SHM shockvel shrinkexceed Shugaev si SiC Siegmund Siepmann Sievers sigI sigmoid Sij Sikandar Silbert Silling Sim Simov Simul simulations Sinkovits Sinnott sinh sinusoid sinusoidally SiO Sirk Sival sizeI sizeJ sizex sj sjplimp sjtu Skomski skyblue Skylake slateblue slategray slater slcsa Slepoy Sliozberg sLL sllod sm smallbig smallint Smallint smallsmall smatb smd SMD smi Smilauer Smirichinski Smit smtbq sna snad snapcoeff snapparam snav Snodin Sodani Soderlind Solaris Solida solv solvated solvation someuser Sorensen soundspeed sourceforge Souza sp spacings Spearot specieslist specular spellcheck Spellmeyer Speybroeck sph SPH spica SPICA Spickermann spinflag splined spparks Sprik Springer springgreen spx spz sqdistharm sqrt src srd sright Srinivasan Srivastava Srolovitz srp srun ss ssao stamoor stamoore stanford Starikov startstep Startstep statcoul statcoulombs statvolt stdin stdio stdlib stdout steelblue Stegailov Steinbach Steinhardt Steinhauser Stepaniants stepwise Stesmans stiffnesses Stillinger stk stl stochastically stochasticity Stockmayer Stoddard Stoermer stoichiometric stoichiometry Stokesian Stoll stopstep Stouch Straatsma Strachan Stratford Strathclyde Straub strcmp streitz Streitz Streiz strerror strided strietz stringstreams strmatch strncmp strstr Stukowski Su subbox Subclassed subcutoff subcycle subcycling subdirectory subdirectories subdomain subdomains subhi sublo Subramaniyan subscripted subscripting sudo Sugaku Suhai Sukumaran Sulc SumI SumN sumsq Sunderland supercell superset supersphere Supinski Sur Surblys surfactant surfactants Suter Sutmann Suzen svn Svoboda sw Swegat swiggle Swiler Swinburne Swol Swope sx Sx sy Sy symplectic symmetrize Synechococcus sys sysdim Syst systemd sz Sz Tabbernor tabinner tabstyle Tadmor Tafipolsky tagID tagint Tainter Tait taitwater Tajkhorshid Tamaskovics Tanaka tanh tanmoy Tanmoy Tartakovsky taskset taubi taylor tb tchain Tchain Tcl Tcom tcsh tdamp tdpd tDPD Tdrude Technol Telsa tempCorrCoeff templated Templeton Tequil ters tersoff Tersoff tesselation tesselations Tetot tex textrm tfac tfmc tfMC tgnpt tgnvt th Thakkar Thaokar thb thei Theodorou Theophile Theor thermalization thermalize thermalized Thermalized thermalizing Thermalizing thermo thermochemical thermochemistry thermodynamically thermopotentiostat Thermophysical thermostatted thermostatting Thermostatting Thes Thess Thexe Thiaville Thibaudeau Thijsse Thirumalai threebody thrid ThunderX thylakoid THz Tieleman Tigran Tij Tildesley Timan timeI timespan timestamp timestamps timestep timestepping timesteps TiN TiO Tirado Tirrell Titer Tji Tk Tkin tloop tlsph tm tmax Tmax tmd tmin Tmin tmp tN tnumeric Tobias Toennies Tohoku tokenizer tokyo tol tomic toolchain toolset topologies Toporov Torder Torino torsions Tosi Toukmaji Toxvaerd tpa tpc tpm tptask tqx tqy tqz traceless tradeoff traj Tranchida transactional transferability translational Translational trate Tref Tretyakov tri triangleflag Tribello triclinic Triclinic triflag trigonal trilinear Trinkle tripflag tris trj trott Trott Trung Trushin tscale Tschopp Tsige Tsrd Tstart tstat Tstop Tsuji Tsuzuki tt Tt TThis ttm ttol tu Tuckerman tue tunable tuple tuples Turkand Tutein tweakable twobody twojmax Tx txt Tyagi typeargs typedefs typeI typeJ typelabel typeN typesafe Tz Tzou ub Uberuaga ubflag Ubflag ubiquitin uca uChem uCond uef UEF ufm Uhlenbeck Ui uind uInfParallel uinp uk ul ulb Uleft Ulomek uloop ulsph Ultrafast uMech umin Umin un unary uncomment uncommented uncompress uncompute underdamped underprediction undump uniaxial uniaxially unimodal uninstall unitarg unitless unittest Universite unix unmaintained unoptimized unordered unpadded unphysical unphysically unreacted unscaled unsets unsmoothed unsolvated unsplit unstrained unstretched untar untilted Unwin uparrow upenn upto Urbakh Urbana UreyBradley Usabiaga usec uSemiParallel userguide username usleep usolve usr util utils utsa Uttormark uval uvm uwo Uzdin vacf Vaid Vaiwala valent Valeriu valgrind Valone valuev Valuev Vanden Vandenbrande Vanduyfhuys varargs varavg variational Varshalovich Varshney vashishta Vashishta vasp vcm Vcm vdfmax vdim vdisplace vdw vdW vdwl vec Vecchio vectorial vectorization Vectorization vectorized Vegt vel Velázquez Ventura venv Verlag verlet Verlet versa Verstraelen ves vf vflag vflow vfrac vhi vibrational Vij Vikas virial Virial virialmode virials virtualenv viscoelastic viscoelasticity viscosities viscously vizplotgui Vj Vkl vlo vmax vmd VMDARCH VMDHOME vn Voigt volfactor Volkov Volpe volpress volumetric von Voro Vorobyov voronoi Voronoi VORONOI Vorselaars Voth Voyiatzis vpz vratio Vries Vsevolod Vsmall Vstream vtarget vtk VTK vtp vtr vtu Vu Vuilleumier vv vx Vx vxcm vxmu vxx vxy vxz vy Vy vycm vyy vyz vz Vz vzcm vzi vzz Waals Wadley wallstyle walltime Waltham Waroquier Wataru wavepacket wB Wbody wca webpage Weckner WeinanE Wennberg Westmere Westview wf wget Whelan whitesmoke whitespace whl Wi Wicaksono widom Widom Wijk Wikipedia wildcard Wildcard wildcards Winkler Wirnsberger wirtes witin Wittmaack wn Wolde workflow workflows Workum Worley Wriggers writedata Wuppertal Wurtzite www wx Wx wy Wy Wysocki wz Wz xa xAVX xb Xc xc xcm Xcm Xcode xCORE xdmf Xeon xflag xhi xHost Xia Xiaohu Xiaowang Xie xk xlat xlo xmax Xmax xmgrace xMIC xmin xml xmovie Xmovie xmu Xmu XP xplane XPlor xrd xs xsc xstk xsu xtc xu Xu xxt xxxxx xy xyz xz xzhou yace Yade yade yaff YAFF Yamada yaml Yanxon Yaser Yazdani Ybar ybox Yc yc ycm Yeh yellowgreen yEs Yethiraj yflag yhi yi ylat ylo ylz ymax ymin yml Yoshida ys ysc ysu yu Yu Yuh yukawa Yukawa Yusof Yuya yx yy yz Zagaceta Zannoni Zavattieri zbl ZBL Zc zc zcm zeeman Zeeman Zemer zenodo Zepeda zflag Zhang Zhen zhi Zhigilei Zhou Zhu zi Zi ziegenhain Ziegenhain zincblende zj Zj zlim zlo Zm zmax zmin zmq zN zs zsc Zsh zst Zstandard zstd Zstd zsu zu zx zy Zybin Zykova zz