aa aat abc abf ABI abi abo Abramyan absTol Acc Accelerys Accelrys acceptor Acceptor acceptors 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 Ahrens Ai Aidan aij aimd airebo Aj ajaramil ajs akohlmey Aktulga al alain Alain Alamos alat Albe alchemical AlCu Alderton Alejandre Aleksei alessandro Alessandro Alexey ali aliceblue Allinger allocator allocators allosws AlO Alonso Alperen alphak alphashrink amap Amatrix AMD amino Amirjalayer Amit amu Amzallag analytical Anders Andrienko Andzelm Ang anglegrad angletangrad angmom angmomx angmomy angmomz Angs anharmonic anharmonicity aniso anisotropic anisotropies anisotropy ansi antiferromagnetic antiquewhite Antisymmetrized antisymmetry anton Antonelli api Apoorva Appl Apu arallel arccos Archlinux arcsin arg arge args argv arrhenius Arun arXiv asin Askari askoose asphere ASPHERE aspherical asphericity Asq assignee assively Asta Astart Astop asub asubrama Asumming atan atc AtC ATC athermal athomps atime atimestep atm atomeye atomfile AtomicPairStyle atomID atomistic atomtypes attogram attograms attrac Atw Atwater atwt augt AuO automagically Auvergne Avalos avalue aveforce Avendano avi AVX awpmd AWPMD Axel Axilrod Ay Ayton Az Azevedo azimuthal Azuri ba Babadi Babaei backcolor backends Baczewski Bagchi Bagi Bagnold Baig Bajaj Bal balancer Balankura Balasubramanian Balatsky Ballenegger Bammann Banna Barashev Barbosa barnes barostat Barostats barostatted barostatting Barostatting Barrat Barros Bartels Bartelt barycenter barye Bashford bashrc Baskes Batra Bayly bb bcc bcolor bdiam bdw Beckman Belak Bellott bem benchmarking Bennet Berardi Beraun Bereau berendsen Berendsen berger Berkowitz berlin Berne Bertotti Bessarab Beutler Bext Bfrac bgq Bh Bialke bicrystal Biersack bigbig bigint Bij bilayer bilayers binsize binstyle binutils biomolecular biomolecule Biomolecules Biophys Biosym biquadratic bisectioning bispectrum Bispectrum bitbucket bitmapped bitmask bitrate bitrates Bitzek Bjerrum Bkappa Blaise blanchedalmond blocksize blueviolet bn bni bo Bochkarev Bochum bocs bodyflag bodyforce bodystyle Bogaerts Bogusz Bohrs boltz Boltzman BondAngle BondBond bondchk bondmax bondscreened bondscreenedspin bondspin bondtype Bonet Bonomi boolean boostostat boostostatting Boresch borophene Botero Botu Bouguet Bourasseau Bourne boxcolor boxhi boxlo boxxhi boxxlo boxyhi boxylo boxzhi boxzlo bp bpclermont bpls bpm BPM br Branduardi Branicio brennan Briels Brien Brilliantov Broadwell Broglie brownian brownw Broyden Brusselle Bryantsev Btarget btype buckPlusAttr buf builtin Bulatov Bureekaew burlywood Bussi Buturigakkwaishi Buyl Bybee bz cadetblue Cagin calc calibrationfunctions calibrationparameters calibre caltech Caltech Camilloni Camiloni Campana 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 centerline centro centroid Centroid centrosymmetry Cercignani cercignanilampis Cerda ceriotti Ceriotti Cerutti cfg CFG cfile CFL cgdna CGDNA cgs cgsdk CGSDK Chaimovich Chalopin Champaign charmm CHARMM charmmfsh charmmfsw charptr Chaudhuri checkbox checkmark checkqeq checksum chemistries Chemnitz Cheng Chenoweth chiral chiralIDs ChiralIDs chirality Cho ChooseOffset chris Christoph Chu chunkID chunksize Ciccotti Cieplak Cii Cij cis civ CKD Clang clearstore Cleary Clebsch clemson Clermont clo Clovertown cmake CMake CMakeLists cmap Cmax cmd cmdlist cmds Cmin cmm CMM cn cN Cn cna cnp cnr coaxstk codebase coeff Coeff CoefficientN coeffs Coeffs cohesionless Coker Colberg coleman Colliex collinear collisional Columic colvars Colvars COLVARS comID Commun compositing compressibility compressive Comput computable compute concat cond conda Conda Condens conf config configfile configurational conformational Connor conp conq ConstMatrix Contrib cooperativity coord Coord CoordN coords coreshell cornflowerblue cornsilk corotate corotation corotational correlator cosineshifted cossq costheta Couette coul coulgauss coulombic Coulombic Coulombics counterion counterions Courant covalent covalently covariance cpp cpu cradius createatoms createAtoms CreateIDs crespi Crespi Critchley crossterm Crowson Crozier Cryst Crystallogr Csanyi csg csh cshrc CSiC csld cslib CSlib cstdio cstdlib cstring cstyle csvr ctrl ctypes Ctypes cuda Cuda CUDA cuFFT CuH Cui Cummins Cundall cundall Curk Cusentino customIDs cutbond cuthi cutinner cutlo cutmax cutoffA cutoffC cuu cv Cv Cval cvar cvff cwiggle cygwin Cygwin cylindrically Cyrot cyrstals cython 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 deallocated debye Debye Decius decompositions decorrelation decrementing deeppink deepskyblue defgrad defn deformable Deissenbeck del delaystep deleteIDs DeleteIDs delflag Dellago delocalization delocalized Delong delr deltaHf dem Dendrimer dendritic Denniston dephase dephasing dequidt Dequidt der dereference derekt Deresiewicz Derjagin Derjaguin Derlet Desbiens Deserno Destree destructor destructors detils Devanathan devel Devemy deviatoric Devine df dfftw DFT dftb dh dhex di dia diag diagonalization diagonalize diagonalized diagonalizers diagonalizing Diallo diblock dichalcogenides Dickel diel Dietz differentiable diffusively diffusivity dihedral dihedrals Dihedrals dihydride Dij dimdim dimensionality dimensioned dimgray dipolar dir Direc dirname discoverable discretization discretized disp dissipative Dissipative distharm dl dlambda DLAMMPS dll dlopen dm dmax Dmax dmg dmi dnf DNi Dobnikar Dobson docenv Dodds dodgerblue dof doi Donadio Donev dotc Doty downarrow doxygen doxygenclass doxygenfunction Doye Doyl dpd DPD dpdTheta dphi DPhil dr dR dragforce Drautz dreiding Dreiding drfourth drho drsquared drude Drude DRUDE dsf dsmc dt dtemp dtgrow dtheta dtshrink du dU Ducastelle Dudarev Duin Dullweber dumpfile Dunbrack Dunweg Dupend Dupont dUs 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 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 Eleftheriou ElementN elementset elementsets elif Elj Ellad ellipsoidflag elong Elsevier Elsner Elstner elt emacs emax Emax Embt emi emol eN endian 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 equil equilibrate equilibrated equilibrates equilibrating equilibration equilibria Equilibria equilization equipartitioning eradius erate erc Ercolessi Erdmann erf erfc Erhart erorate erose erotate errno Ertas ervel eshelby Eshelby eskm Espanol esph estretch esu esub esw et etag etap ETarget ethernet etol etot etotal etube eulerian Eulerian eulerimplicit Europhys ev eV eval evals evalue Evanseck evdwl evec evecs evector Everaers Evgeny evirials ew ewald Ewald excitations excv exe executables extep extrema exy ey ez faceset facesets factorizable factorizations Fahrenberger Faken Farago Fasolino Fath Fava fbMC Fc fcc fcm fd Fd fdotr fdt fe Fehlberg Fellinger femtosecond femtoseconds fene Fennell fep FEP fermi Fermionic Ferrand fexternal Fexternal ffield ffl fflush ffmpeg FFmpeg ffplay fft fftbench fftMPI fftw fgets fhg Fi Fichthorn Fickian fieldname figshare Fij filelink filename Filename filenames Filenames fileper filesystem filesystems Fily Fincham Finchham fingerprintconstants fingerprintsperelement Finnis Fiorin fixID fj Fji flagfld flagHI flaglog flagN flagVF fld floralwhite Florez flv fm fmackay fmag fmass fmatch fmm fmt fmtlib fmx fmy fmz fN Fn fname fno Fnudge foces Fock Fogarty Foiles fopenmp forceclear forestgreen formatarg formulae Forschungszentrum fortran Fortran Fosado fourier fp fphi fPIC fplo Fqq Fraige framerate Frauenheim Fraunhofer fread Freitas Frenkel Friedrichs fs fsh fstyle fsw ftm ftol fuer fugacity Fumi func funcs functionalities functionals funroll Furuholt fx fy fz Gabor Gahler gainsboro Galindo gamA gammaA gammaFactor gammaR gamR Gan GaN ganzenmueller Ganzenmuller Gao Gathert Gaus gauss gaussian gaussians Gaussians Gavhane Gawlik gayberne gcc gcmc gdot GeC Geier gencode Geocomputing georg Georg Geotechnica germain Germann Germano gerolf Gerolf Gershgorin getrusage getter gettimeofday gewald Gezelter Gflop gfortran ghostwhite Giacomo gif gifsicle Gillan Gingold Gissinger github gjf gjwagne gl gladky Gladky gld gle globbing Gloor Glosli Glotzer gmail gmake gmask Gmask GMock gmres gneb GNEB Goldfarb Gompper Gonzalez-Melchor googlemail googletest Gordan Goudeau GPa GPL gpu gpuID gpus gradgradflag gradV GradVidottan graining Graining Grama grana granregion graphene Greathouse greenyellow Greffet grem gREM Grest Grigera Grimme grmask Grmask gromacs Gromacs gromos Gronbech Groot groupbig groupbit grp Grueneisen gsmooth gstyle GTL Gubbins Guenole Guericke gui Guillope Gumbsch Gunsteren Gunzenmuller Guo gw gyromagnetic gz gzip gzipped Haak Hafskjold halfstepback Halperin Halver Hamaker Hamel Hammerschmidt Hanley haptic Hara Harpertown Harting Hartree Hartrees Hasan Hashtable Haswell Haugk Hayoun Hayre hbar hbcut hbn hbnewflag hbond hcp hdnnp HDNNP Hearn heatconduction Hebbeker Hebenstreit Hecht Heenen Hendrik Henin Henkelman Henkes henrich Henrich Hermitian Herrmann Hertizian hertzian Hertzsch heterostructures hexahedrons hexatic hexorder Heyes HfO hftn hgrid hhmrr Hibbs Higdon hiID Hijazi Hilger Hinestrosa hipFFT histo histogrammed histogramming hma hmaktulga hoc Hochbruck Hofling Holian Holm holonomic Homebrew hooke hookean Hookean hostname hotpink Houlle howto Howto Hoy Hoyt hplanck Hs hstyle html hTST https hu Hueckel Huetter Hugonio hugoniostat Hugoniostat Hugoniot Hura hux hwloc hx hy hydrophobicity hydrostatic hydrostatically hydroxyl Hynninen Hyoungki hyperdynamics hyperplane hyperradius hyperspherical hysteretic hz IAP iatom Ibanez ibar ibm icc ico icosahedral idealgas IDR idx ie ielement ieni ifdefs iff ifort Ihle ij ijk ijkl ik Ikeshoji Ilie ilmenau Ilmenau ilp Ilya im Im imageint Imageint Imagemagick imd Impey impl impropers Impropers imulator includelink incompressible incrementing indenter indenters indianred indices inertiax inertiay inertiaz infile infty inhomogeneities inhomogeneous init initialdelay initialisms initializations InitiatorIDs initio InP inq inregion instantiation Institut integrators Integrators intel intelmpi interal interatomic Interatomic interconvert interfacial interial interlayer intermolecular Interparticle interstitials intertube Intr intra intralayer intramolecular ints inv invariants inversed ionizable ionocovalent 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 ixx Ixx ixy Ixy ixz Ixz iy iycm iyy Iyy iyz Iyz iz izcm ized Izrailev Izumi Izvekov izz Izz 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 Jochim Jonsson Jorgensen jp jparam jpeg jpeglib jpg JPG jpl json Jth jtranch jtype jtypeN Juelich Julien junghans Junghans Jungnickel Jupyter Justo Jusufi Jx Jy Jz jzimmer Kadiri Kai Kalia Kamberaj Kantorovich Kapfer Karls Karlsruhe Karniadakis Karplus Karttunen kate Katsnelson Katsura Kaufmann Kawata Kaxiras Kayser kb kB kbit kbits kcal kcl Kd KDevelop ke KE Keblinski Keefe Keffer keflag Keir Kelchner Kelkar Kemper kepler keV Keyes Khersonskii Khrapak Khvostov Ki Kikugawa kim kinetostats Kirkwood kJ kk Klahn Klapp Kloss Kloza kmax Kmax KMP kmu Knizhnik knl kofke Kofke Kohlmeyer Kohn kokkos Kolafa Kollman kolmogorov Kolmogorov Kondor konglt Koning Kooser Korn Koskinen Koslowski Kosovan Koster Kosztin Koziol Kp kradius Kraker Kraus Kremer Kress Kronik ksh kspace Kspace KSpace KSpaceStyle Kspring kT kTequil kth Kth kTln ktypeN Kub Kubo Kumagai Kumar Kurebayashi Kuronen Kusters Kutta Kuznetsov kx Lachet Lackmann Ladd lagrangian lambdai LambdaLanczos lamda lammps Lammps LAMMPS lammpsbin lammpsplot lammpsplugin Lamoureux Lampis 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lmpqst lmpsdata Lmpsdata lmptype LMT ln localhost localTemp localvectors Loewen logfile logfreq logicals loID Lomdahl Lond lookup lookups Lookups LoopVar Lorant lorenz Los lossless lossy Lozovik lps lpsapi lrt lsfftw ltbbmalloc Lua lubricateU lucas lucy Luding Luijten lunit Lunkad Lussetti Lustig lval lwsock lx ly Lybrand lyon Lysogorskiy Lyulin lz lzma Maaravi machdyn MACHDYN Mackay Mackrodt MacOS Macromolecules macroparticle Madura Magda Magdeburg magelec Maginn magneton magnetons mainboard mainboards makefile Makefile makefiles Makefiles makelist makepkg Makse malloc Malolepsza Manby Mandadapu Mandelli Manh manifoldforce Manolopoulos manpages manybody MANYBODY Maras Marchetti Marchi Mariella Marinica Marrink Marroquin Marsaglia Marseille 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 meam MEAM meamf meanDist mech 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 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 Mises Mishin Mishra mistyped mistyrose Mj mK mkdir mkv mlength mliap mliappy mlparks Mniszewski mnt mobi modc Modell modelled modelling Modelling Modine mofff MOFFF Mohd Mohles mol Mol molfile Molfile MolPairStyle moltemplate momb Monaghan Monaghans monodisperse monodispersity monopole monovalent Montalenti Montero Mora Morefoo Morfill Mori Moriya morris Morriss morse Morteza Mosayebi Moseler Moskalev Moustafa mov mpi MPI mpicc mpiCC mpich mpicolor mpicxx mpiexec mpiio mpirun mplayer mps mradius Mrovec Mryglod mscg MSCG msd msi MSI msm msse msst Mtchell Mth mtk Mtotal muB Muccioli mui Mukherjee Mulders Müller mult multi multibody Multibody multicenter multicentered multicmd multicomponent multicore multielectron multinode multiphysics multiscale multisectioning multithreading Multithreading multivalent Mundy Murdick Murtola Murty Muser mutexes Muto muVT mux muy muz mv mV Mvapich mvh mvv MxN myCompute myIndex mylammps MyPool mysocket mySpin myTemp myVec na nabla Nagaosa Nakano nall namedtuple namespace namespaces nan NaN Nandor nangles 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nocite nocoeff nodeless nodeset nodesets Noehring Noffset noforce Noid nolib nonequilibrium nongauss nonGaussian nonlocal Nonlocal Noordhoek nopreliminary Nord norder Nordlund normals Noskov noslip noticable Nout noutcol Noutput noutrow Novik Novint np Npair Npairs nparams nparticle npernode nph NpH Nphi nphug nprocs Nprocs npt nr Nr Nrecompute Nrepeat nreset Nrho Nroff nrow nrun ns Ns Nsample Nskip Nspecies nsq Nstart nstats Nstep Nsteplast Nstop nsub Nsw Nswap nt Nt Ntable ntheta nthreads ntimestep Ntptask Ntriples ntris Ntype ntypes Ntypes nucleotide nucleotides nullptr num numa numactl numdiff numericalfreedom numerics numpy Numpy Nurdin Nvalue Nvaluelast Nvalues nvc nvcc nve nvidia nvk nvt Nwait nwchem nx Nx nxnodes ny Ny nz Nz ocl octahedral octants Ohara O'Hearn ohenrich ok Okabe Okamoto O'Keefe OKeefe oldlace olecular Oleinik Olfason olivedrab Ollila Olvera omegaDD omegax omegay omegaz Omelyan omp OMP oneAPI onelevel oneway onlysalt onn ons OO Oord opencl openKIM openmp OpenMP openmpi opls Oppelstrup optimizations orangered organometallic orientational orientationsFile orientorder Orlikowski ornl Ornstein Orsi ortho orthonormal orthorhombic Ortner os oso Otype Ouadfel Ouldridge outfile outmost outputss Ouyang overdamped overlayed Ovito oxdna oxDNA oxrna oxRNA packings padua Padua pafi PairIJ palegoldenrod palegreen paleturquoise palevioletred Panagiotopoulos Pandit Papaconstantopoulos papayawhip paquay Paquay parallelepiped Parallelizable parallelization parallelized parallelizing param parameterization parameterizations parameterize parameterized params ParaView parmin Parrinello Partay Particuology Pascuet pastewka Pastewka pathangle pathname pathnames Patomtrans Pattnaik Pavese Pavia Paxton pbc pc pchain Pchain pcmoves Pdamp pdb pdf pdfs pdim pe Peachey peachpuff Pearlman Pedersen peID PEigenDense Peng peptide peratom Pergamon peri peridynamic Peridynamic peridynamics Peridynamics perl permittivity perp Perram persp Persp peru Peskin Pettifor pfactor pgi ph Philipp Phillpot Philos phiphi phonon phonons phophorous phosphide Phs Physica physik pI Piaggi picocoulomb picocoulombs picogram picograms picosecond picoseconds pid piecewise Pieniazek Pieter pIm pimd Piola pIp Pisarev Pishevar Pitera pj pjintve pKa pKb pKs planeforce Plathe Plimpton plog ploop PloS plt plumedfile pmb pmcmoves Pmolrotate Pmoltrans pN png Podhorszki Poiseuille poisson Polak polarizabilities polarizability polarizable Polarizable polarizables polarizer Politano Politecnico polyA polybond polydisperse polydispersity polyelectrolyte polyhedra Polym polymorphism popen Popov popstore Poresag pos Poschel posix postfix postfixed postfixes Postma Potapkin potentiostat potin Pourtois powderblue PowerShell ppn pppm Prakash Praprotnik prd pre Pre prec precession prefactor prefactors prepend prepended preprint printf printflag priori Priya proc Proc procs progguide Prony ps Ps pscreen pscrozi pseudodynamics pseudopotential pSp Pstart Pstop pstyle Ptarget pth pthread pthreads ptm PTM ptol ptr PTX pu purdue Purohit pushstore pvar pw pwqmmm px Px pxx Pxx pxy Pxy pxz py Py pydir pylammps PyLammps pymbar pymodule pymol 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 Quant quartic quat quaternion quaternions quati quatj quatk quatw queryargs Queteschiner quickmin qw qx qy qz radialscreened radialscreenedspin radialspin radian radians Rafferty rahman Rahman Ralf Raman ramped ramping Ramprasad Randisi randomizations rann RANN Rapetti Raphson Rappe Ravelo rc Rc Rci Rcm rcmax Rcmx Rcmy Rco Rcut rcutfac rdc rdf RDideal rdx reacter Readline README real_t realtime realTypeMap reamin reax reaxff ReaxFF REAXFF rebo recurse recursing Ree refactored refactoring reflectionstyle Reinders reinit relaxbox relink 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 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 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 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 rxnsum ry Ryckaert Rycroft Rydbergs rz Rz Sabry saddlebrown Sadigh saed safezone Safran Sagui Saidi saip Salanne Salles sandia Sandia sandybrown sanitizer Sanyal Sarath sc scafacos SCAFACOS scalability scalable Scalable scalexy scalexz scaleyz Scalfi Schaik Scheid Schilfgarde Schimansky Schiotz Schlitter Schmid Schoen Schotte Schratt Schulten Schunk Schuring Schwen Sci screenshot screenshots Scripps Scripta sd sdk sdpd SDPD se seagreen Secor sectoring sed segmental Seifert sellerio Sellerio Semaev semiaxes semimetals Semin Sensable Sep seqdep Serpico setfl setforce Sethna setmask Setmask setpoint setvel sfftw sfree Sg Shan Shanno 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 sinusoid sinusoidally SiO Sirk Sival sizeI sizeJ sizex sj sjplimp sjtu Skomski skyblue Skylake slateblue slategray slater Slepoy Sliozberg sLLG sllod sm smallbig smallint Smallint smallsmall smatb smd SMD smi Smilauer Smirichinski Smit smtbq sna snad snapcoeff snapparam snav Snodin Sodani Soderlind Solida solvated solvation someuser Sorensen soundspeed sourceforge Souza sp spacings Spearot specular spellcheck Spellmeyer Speybroeck sph SPH Spickermann 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 subhi sublo Subramaniyan subscripted subscripting sudo Sugaku Suhai Sukumaran Sulc sumsq Sunderland supercell superset supersphere Supinski Surblys surfactant surfactants Suter Sutmann Suzen svn Svoboda sw Swegat swiggle Swiler Swinburne Swol Swope sx Sx sy Sy symplectic Synechococcus sys sysdim Syst systemd sz Sz Tabbernor tabinner 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 Tetot tex tfac tfmc tfMC tgnpt tgnvt th Thakkar Thaokar thb thei Theodorou Theophile Theor thermalization thermalize thermalized Thermalized thermalizing Thermalizing thermo thermochemical thermochemistry thermodynamically Thermophysical thermostatted thermostatting Thermostatting Thes Thess Thexe Thiaville Thibaudeau Thijsse Thirumalai threebody thrid ThunderX thylakoid THz Tigran Tij Tildesley timeI timespan timestamp timestamps timestep timestepping timesteps TiN TiO Tirrell Titer Tji Tk Tkin tloop tlsph tmax Tmax tmd tmin Tmin tmp tN Tobias Toennies Tohoku tokenizer tokyo tol tomic toolchain 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 typeN typesafe Tz Tzou ub Uberuaga uca uChem uCond uef UEF ufm Uhlenbeck Ui uInfParallel uk ul ulb Uleft Ulomek uloop ulsph Ultrafast uMech umin Umin un unary uncomment uncompute underprediction undump uniaxial uniaxially unimodal unitarg unitless Universite unix unmaintained unoptimized unpadded unphysical unphysically unreacted unscaled unsets unsmoothed unsolvated unsplit unstrained untar untilted Unwin uparrow upenn upto Urbakh Urbana Usabiaga usec uSemiParallel userguide username usleep usr util utils utsa Uttormark uval uvm uwo Uzdin vacf Vaid Vaiwala valent Valeriu valgrind Valone valuev Valuev Vanden Vandenbrande Vanduyfhuys varargs varavg Varshalovich Varshney vashishta Vashishta vasp vcm Vcm vdfmax vdim vdisplace vdW vdwl vec vectorial vectorization Vectorization vectorized Vegt vel Velázquez venv Verlag verlet Verlet versa Verstraelen ves vflag 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 vy Vy 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