aa aat Abascal abc abf ABI abi abo Abramyan absTol Acad Acc Accelerys Accelrys acceptor Acceptor acceptors accessor accomx accomy accomz accuracies ach ackland Ackland acks acolor acos acs Acta actinide activationfunctions acylindricity addforce Addington addstep 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 aliphatic Allera Allinger allocatable allocator allocators allosws AlO alo Alonso Alperen alphak alphashrink amap Amatrix AMD amino Amirjalayer Amit amsmath amu Amzallag Anandakrishnan analytical Anders Andric Andrienko Andzelm Ang anglegrad anglelist angleoffset angletangrad angmom angmomx angmomy angmomz Angs anharmonic anharmonicity aniso anisotropic anisotropies anisotropy ansi antiferromagnetic antiquewhite Antisymmetrized antisymmetry anton Antonelli anysize api apip APIP apolar Apoorva Appl Appshaw apptainer Apu arallel arccos Archlinux arcsin arg arge args argv Armv arrhenius Arun arXiv asin Askari askoose asphere ASPHERE aspherical asphericity Asq assignee assively associativity 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 atype augt AuO automagically Auvergne Avalos avalue avec avecx avecy avecz aveforce Avendano Averett avi AVX awpmd AWPMD ax Axel Axilrod Ay ay Ayton Az az Azevedo azimuthal Azuri ba Babadi Babaei backcolor Baczewski Bagchi Bagi Bagnold Baig Bajaj bak Bal balancer Balankura Balasubramanian Balatsky Ballenegger Bammann Banna Barashev Barbosa barnes barostat Barostats barostatted barostatting Barostatting Barrat Barros Bartels Bartelt barycenter barye basename Bashford bashrc Baskes Batatia Batra Bayly bb bcc bcolor bdiam bdw Becke Beckman Becton Behler Belak Bellott bem benchmarking Bennet Berardi Beraun Bereau berendsen Berendsen berger Berkowitz berlin Berne Bertotti Bessarab bessel Beutler Bext Bfrac bgq Bh bhi Bialke biaxial bicrystal Biersack biga bigbig bigint Bij bilayer bilayers binsize binstyle binutils Biomech biomolecular biomolecule Biomolecules biomolecules Biophys Biosym biquadratic bisectioning bispectrum Bispectrum bitbucket bitmapped bitmask bitorsion bitrate bitrates Bitzek Bjerrum bjm Bkappa blabel Blaise blanchedalmond blo blocksize blueviolet bn bni bnumeric bo Bochkarev Bochum bocs bodyflag bodyforce bodystyle Bogaerts Bogoliubov Bogusz Bohrs boltz Bomont BondAngle BondBond bondchk bondlist bondmax bondscreened bondscreenedspin bondspin bondtype Bonet Bonomi boolean boostostat boostostatting Boresch borophene bosonic bosons Botero Botu Bouguet Bourasseau Bourne boxcolor boxhi boxlo boxxhi boxxlo boxyhi boxylo boxzhi boxzlo bp bpclermont bpls bpm BPM br Braems Branduardi Branicio brennan Bretonnet Briels Brien Brilliantov Brizi Broadwell Broglie brownian brownw Broyden Bruenger Bruskin Brusselle Bryantsev Btarget btype buckPlusAttr buf builtin Bulacu Bulatov Bulkley Bureekaew burlywood Bussi Buturigakkwaishi Buyl bvec bvecx bvecy bvecz Bybee bz Cadarache cadetblue Caen Cagin calc calibrationfunctions calibrationparameters calibre caltech Caltech Camilloni Camiloni Campana Cangi Cao Cappelletti Capolungo Caro cartesian Cas Casavecchia 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 clearstep 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 COH COLVARS comID Commun compositing compressibility compressive Comput computable compute concat cond conda Conda Condens conductivities conf config configfile configurational conformational Connor conp conq const ConstMatrix Contrib cooperativity coord Coord CoordN coords coreshell cornflowerblue cornsilk corotate corotation corotational correlator Cosecant cosineshifted cossq costheta Couette coul coulgauss coulombic Coulombic Coulombics counterion counterions CountI CountN Courant covalent covalently covariance cp cpp cpu cradius Cramer createatoms createAtoms CreateIDs crespi Crespi Creuze Critchley crossterm Crowson Crozier Cryst Crystallogr Csanyi csc csg csh cshrc CSiC csld cslib CSlib csp cstdio cstdlib cstring cstyle csvr ctest ctilde ctip ctrl ctrn ctypes Ctypes cuda Cuda CUDA cuFFT CuH Cui Cummins cumulants 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 dataset datums Davidchack Daw dcd dcub Dcut de dE De deallocate deallocated deallocation 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 dihedrallist dihedrals Dihedrals dihydride Dij dimdim dimensionality dimensioned dimgray dipolar dipoleflag dir Direc dirname Dirkmann 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 docstrings 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 dvipng 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 electronegativities electronegativity electroneutral electroneutrality Eleftheriou ElementN elementset elementsets elif Elj Ellad ellipsoidflag elong Elsevier Elsner Elstner elt emacs emax Emax Embt emi Emilie 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 Equilibria equilization equipartitioning eradius erate Ercolessi Erdmann erf erfc erforce Erhart erorate erose erotate errno Ertas ervel eshelby Eshelby eskm Espanol esph espin estretch esu esub esw esynch et etag etap ETarget ethernet etol etot etotal etube eulerian Eulerian eulerimplicit Europhys ev eV eval evals evaluator evalue Evanseck evdwl evec evecs evector Everaers Evgeny evirials ew ewald Ewald ewaldflag excitations excv exe executables extep extractable extrema extxyz exy ey ez faceset facesets factorizable factorizations Fahrenberger Falk Faken Farago Fasolino Fath Fava fbMC Fc fcc fcm fd Fd fdotr fdt fe Fehlberg Feldman Fellinger femtosecond femtoseconds fene Feng Fennell fep FEP fermi fermion fermions Fermionic Ferrand fexternal Fexternal ffast 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 Finkelstein Fint fingerprintconstants fingerprintsperelement finitecutflag Finnis Fiorin fitpod fivebody fixcom fixID fj Fji flagfld flagHI flaglog flagN flagVF flang flatpak fld floralwhite Florez flv fm fmackay fmag fmass fmatch fmm fmmode fmt fmtlib fmx fmy fmz fN Fn fname fncychap fno Fnudge foces Fock Fogarty Foiles fontawesome fopenmp forceclear forestgreen formamide formatarg formulae Forschungszentrum fortran Fortran Fosado fourbody fourier fp fphi fPIC fplo fprintf Fqq Fraige framerate Frauenheim Fraunhofer fread Freitas Frenkel Friedrichs fs fsaa fsh fstyle fsw ftm ftol fuer fugacity Fu 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 Geesthacht Geier gencode Geocomputing georg Georg Geotechnica germain Germann Germano gerolf Gerolf Gershgorin getrusage getter gettimeofday geturl gewald Gezelter gfile gflag Gflop gfortran ghostneigh ghostwhite Ghahremanpour Giacomo GiB gif gifsicle Gillan Gingold Gissinger github Giusti GJ gjf gjwagne gl gladky Gladky gld gle globbing Gloor Glosli Glotzer gmail gmake gmap gmask Gmask GMock gmres gname gneb GNEB Godehard Goerigk Goga Goldfarb Gompper Gonzalez-Melchor Goodsell googlemail googletest Gordan Goryaeva Goudeau GPa GPL gpu gpuID gpus gradgradflag gradV GradVidottan graining Graining Grama grana granregion graphene Gravelle Greathouse greenyellow Greffet grem gREM Grepl 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 gyre gyromagnetic gz gzip gzipped Haak Hafskjold halfstepback halgren Hallil Halperin Halver Hamaker Hamel Hammerschmidt Hanley Hanna haptic Haque Hara Harpertown Harting Hartree Hartrees Hasan Hashtable Haswell Haugk Hayoun Hayre hbar hbcut hbn hbnewflag hbond hcp hdnnp HDNNP Hearn Heaviside heatconduction heatflow Hebbeker Hebenstreit Hecht Heenen heFFTe Hendrik Henin Henkelman Henkes Hennig henrich Henrich Hermitian Herrmann Hershchel Hertizian hertzian Hertzsch heterostructures hexahedrons hexatic hexorder Heyes HfO hftn hgrid hhmrr Hibbs Higdon Higer hiID Hijazi Hilger Hinestrosa hipCUB 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 http https hTST https hu Hueckel Huetter Hugonio hugoniostat Hugoniostat Hugoniot Hura hux hwloc hx hy hydronium hydrophobicity hydrostatic hydrostatically hydroxyl Hynninen Hyoungki hypcap hyperdynamics hyperparameters hyperplane hyperradius hyperref hyperspherical hysteretic hz IAP iatom Ibanez ibar ibm icc iceblue ico icosahedral idealgas IDR idx ie ielement ieni ifdef ifdefs iff ifort ihi Ihle ij ijk ijkl ik Ikeshoji ilabel Ilie ilmenau Ilmenau ilo ilp Ilya im Im imageint Imageint Imagemagick imagename imd Immel Impey impl improperlist impropers Impropers imulator includelink incompressible incompressibility incrementing indenter indenters indianred indices inertiax inertiay inertiaz infile infty inhomogeneities inhomogeneous init initialdelay initialisms initializer initializations InitiatorIDs initio InP inq inregion instantiation Institut integrators Integrators intel intelmpi interal interatomic Interatomic interconvert interfacial interial interlayer intermolecular interoperable Interparticle interpretable 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 Izadi Izrailev Izumi Izvekov izz Izz Jacobian Jacobsen Jadhao Jadhav Jagielski jagreat Jahn Jalalvand james Janssen Janssens Jaramillo Jarzynski jatempl javascript jcc jcp jea jec Jeffers jewett Jewett jgissing ji Jiang Jiahao Jiao jik JIK jku jN Joanes Joannopoulos Jochim Jonsson Jorgensen jp jparam jpclett 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 Kamrin Kantorovich Kapfer Kapil Karhunen Karls Karlsruhe Karniadakis Karplus Karttunen kate katom Katsnelson Katsura Kaufmann Kawata Kaxiras Kayser kb kB kbit kbits kbond kcal kcl Kd KDevelop ke KE Keblinski Keefe Keffer keflag Keir Kelchner Kelkar Kemppainen Kemper kepler Kemppainen keV Keyes keyfile Kfoury Khersonskii Khrapak Khvostov Ki Kikugawa kim kinetostats Kirkwood kJ kk Klahn Klapp Kloss Kloza kmax Kmax kMC KMP kmu Knizhnik knl kofke Kofke Kohlmeyer Kohn kokkos Kolafa Kollman kolmogorov Kolmogorov Kolotinskii Kondor konglt Koning Kooser Korn Koskinen Koslowski Kosovan Koster Kosztin Koziol Kp kradius Kraker Krass Kraus Kremer Kress Krieg Kronik ksh kspace Kspace KSpace KSpaceStyle Kspring kstyle kT kTequil kth Kth kTln ktypeN Kub Kubo Kuksenok Kumagai Kumar Kurebayashi Kuronen Kusters Kutta Kuznetsov kx labelmap Labelmap Lachet Lackmann Ladd lagrangian Lalli lambdai LambdaLanczos Lambrecht lamda lammps Lammps LAMMPS lammpsbin lammpsdata lammpsplot lammpsplugin Lamoureux Lampis Lanczos Lande Landron Landsgesell Langer langevin Langevin Langston lanl larentzos Larentzos Laroche lars latboltz LATBOLTZ latencies Latour latourr lattce Laupretre Lauriat lavenderblush lawngreen layersize lB lbfgs lbl LBtype lc lcbop ld lda ldfftw ldg lebedeva Lebedeva Lebold Lechman Legrand Lehoucq Leimkuhler Leite leiu lemonchiffon Lenart lennard Lennard Lenosky Lenz Leoni Lett Leuven Leven Lewy LF LGPL lgvdw Liang libatc libAtoms libawpmd libch libcolvars libcurl libdir libdl libfftw libgcc libgpu libinqmdi libjpeg libkim liblammps Liblammps liblink libmeam libmessage libmpi libmpich libnuma libplumed libplumedKernel libpng libpoems libqemdi libqmmm librar libreax libs Lifshitz ligand lightblue lightcoral lightcyan lightgoldenrodyellow lightgreen lightgrey lightpink lightsalmon lightseagreen lightskyblue lightslategray lightsteelblue lightyellow Likhtman limegreen linalg Lindahl lineflag lineforce linesearch linux Liouville Lisal listfile Littmark Liu Livermore lj llammps lld LLVM lm lmp lmpptr lmpqst lmpsdata Lmpsdata lmptype LMT ln localhost localTemp localvectors Loeve Loewen logfile logfreq logicals loID Lomdahl Lond lookup lookups Lookups LoopVar Lorant lorenz Los lossless lossy Lozovik lps lpsapi lr lrt lsfftw lt ltbbmalloc Lua lubricateU lucas lucy Luding Lueptow Luijten lunit Lunkad Lussetti Lustig lval lwsock lx ly Lybrand Lykotrafitis lyon lyp Lysogorskiy Lyulin lz lzma Maaravi machdyn MACHDYN Mackay Mackrodt MacLaurin macOS Macromolecules macroparticle Maday Madura Magda Magdeburg magelec Maginn magneton magnetons maha Mahalanobis Mahoney Maillet mainboard mainboards makefile Makefile makefiles Makefiles makelist makepkg Makse Malavasi malloc Malolepsza Manby Mandadapu Mandelli Manh manifoldforce Manolopoulos manpages manybody MANYBODY mapID mapIDs Maras Marchetti Marchi Mariella Marinica Markland Marko Marrink Marroquin Marsaglia Marseille Martyna mary marys Masaglia Mashayak Massimilliano massless masstotal Masuhiro Matchett Materias mathbf mathjax matlab Matom 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 meltable 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 modularity 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 Morawietz 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 Mulliken mult multi multibody Multibody multicenter multicentered multicmd multicomponent multicore multielectron multinode multinomial multiphysics Multipole multiscale multisectioning multithreading Multithreading multivalent Mundy Murdick Murtola Murty Muser Mussenbrock mutexes Muto muVT mux muy muz mv mV Mvapich mvh mvv mwlc MxN myCompute myIndex mylammps myMultiply MyPool mysocket mySpin myTemp myVec na nabla Nagaosa Nakano nall namedtuple namespace namespaces nan NaN Nandor nanglelist nangles Nangletype nangletypes Nangletypes nano nanoindentation Nanoletters nanomechanics nanometer nanometers nanoparticle nanoparticles nanopores nanostructures nanotube Nanotube nanotubes nanowires Narulkar nasa nasr natively Natoli natoms Natoms Natomtype Nattempt navajowhite Navier nb Nbin Nbins nbodies nbody Nbody nbond nbondlist nbonds nbondtype Nbondtype nbondtypes Nbondtypes nBOt nbrhood Nbtypes Nbytes nc Nc nclasses nchunk Nchunk ncoeff ncol ncorr ncount nd ndactrung ndescriptors ndihedrallist ndihedrals Ndihedraltype ndihedraltypes Ndirango ndof Ndof Ndouble ndx neb needspace neel Neel Neelov Negre Negrut nelem Nelement Nelements nelems nellipsoids nemd netapp netcdf netstat Nettleton networklayers Neumann Nevent nevery Nevery Nevins newfile Newns newstep newtype nextsort Neyts Nf nfft nfile Nfile Nfreq ng Ng nghost Nghost Ngpu ngpus Ngyuen nh nharmonic nhc nhi NiAlH Nicklas Niklasson Nikolskiy nimproperlist nimpropers Nimpropertype nimpropertypes Ninteger NiO Nissila nist Nitol nitride nitrides niu Nk nktv nl nlayers nlen Nlimit nlines Nlines nlist nlo nlocal Nlocal Nlog nlp nm Nm nmax Nmax nmc nmin Nmin Nmols nn nnodes npits npj nmpimd nO Nocedal nocite nocoeff nodeless nodeset nodesets Noehring nofix Noffset noforce noguess Noid nolib nonaffine nonequilibrium nongauss nonGaussian nonlocal Nonlocal Noordhoek noprecond nopreliminary Nord norder Nordlund noremap normals normx normy normz Noskov noslip notational noticable Nout noutcol Noutput noutrow Novik Novint np Npair Npairs nparams nparticle npernode nph NpH Nphi nphug nprocs Nprocs npt nr Nr Nrecent Nrecompute Nrepeat nreset Nrho Nroff nrow nrun ns Ns Nsample Nskip nspecial Nspecies 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 obabo ochre ocl octahedral octants Odegard Og Ohara O'Hearn ohenrich ok Okabe Okamoto Okazaki O'Keefe OKeefe oldlace oldtop olecular Oleinik Olfason olivedrab Ollila Olvera omegaDD omegax omegay omegaz Omelyan omp OMP ondulated oneAPI onebody onelevel oneMKL oneway onlysalt ons Onufriev 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 Ottino Otype Ouadfel Ouldridge outfile outmost outputss Ouyang overdamped overlayed Ovito oxdna oxDNA oxhi oxlo oxrna oxRNA packings padua Padua pafi PairIJ palegoldenrod palegreen paleturquoise palevioletred Panagiotopoulos Pande Pandit Papaconstantopoulos papayawhip paquay Paquay parallelepiped parallelepipeds Parallelizable parallelization parallelized parallelizing param parameterization parameterizations parameterize parameterized params ParaView parmin Parrinello Partay Particuology Pascuet pastewka Pastewka pathangle pathname pathnames Patera Patkowski Patomtrans Pattnaik Pavese Pavia Paxton pbc pbe pc pcg pchain Pchain pcmoves Pdamp pdb pdf pdfs pdim pe Peachey peachpuff Pearlman Pedersen pedone Pedone peID PEigenDense Peng peptide peratom Perf Pergamon pergrid peri peridynamic Peridynamic peridynamics Peridynamics Periole perl permittivity perp Perram persp Persp perturbative peru Peskin Pettifor pewald pfactor pflag pgi ph Philipp Phillpot Philos phiphi phonon phonons phophorous phosphide Phs Physica physik pI Piaggi picocoulomb picocoulombs picogram picograms picosecond picoseconds pict pid piecewise Pieniazek Pieter pIm pimd pimdb Piola pIp pipelining Pirani pirani Pisarev Pishevar Pitera pitorsion pj pjintve pKa pKb pKs planeforce plastically Plathe Plimpton plog ploop PloS plt plumedfile plyp pmb pmcmoves pme pmf Pmolrotate Pmoltrans pN png podd Podgornik Podhorszki Poiseuille poisson Polak polarizabilities polarizability polarizable Polarizable polarizables polarizer Politano Politecnico polyA polybond polydisperse polydispersity polyelectrolyte polyhedra Polym polymorph polymorphism Ponder Ponte popen Popoola Popov popstore Poresag pos Poschel posix postfix postfixed postfixes Postma Potapkin potentiostat potin Pourtois powderblue PowerShell ppme ppn pppm pppmflag Prakash Praprotnik prd pre Pre prec precession precond prefactor prefactors prepend prepended preprint printf printflag priori Priya proc Proc procs procgrid progguide Prony ps Ps pscreen pscrozi pseudocode Pseudocode pseudodynamics pseudoparticle pseudopotential psllod pSp pSPICA 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 pyargs pydir pylammps PyLammps pymbar pymodule pymol PySCF pythonic pytorch pyy Pyy pyz pz Pz pzz Pzz qbmsst qcore qdist qe qE qeff qelectron qeq qeqr Qamar QeQ QEq QEqR qfactor qfile qi Qi qj Qj Ql qm Qmin qmmm qmol qoffload qopenmp qoverride qqr qqrd Qsb qtb qtpie quadratically quadrupolar quadrupole quadrupoles Quant quartic quat quaternion quaternions quati quatj quatk quatw queryargs Queteschiner quickmin quintic qw qx qy qz Rackers Radeon radi radialscreened radialscreenedspin radialspin radian radians radiative radj Rafferty rahman Rahman Rajamanickam Rakhsha 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 reStructuredText Restrepo rethrowing Revenga rewrap rezwanur rfac rfile rflag rg Rg Rhaphson Rhe rheo 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 Rizzi 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 rnflag rng rNEMD ro rocFFT Rochus Rockett rocksalt Rodrigues Rohart Roncaratti Ronchetti Ronevich Rosati Rosato Rosenberger Rossi Rossky rosybrown rotationally Rotenberg Rothenburg Rovigatti royalblue rozero Rperp Rr rRESPA Rsi Rso Rspace rsort rsq rst rstyle rsurf Rubensson Rubia Rud Rudd Rudra Rudranarayan Rudzinski Runge runtime Rupp Rutuparna rx rxd rxnave rxnbond rxnsum ry Ryckaert Rycroft Rydbergs Ryzen rz Rz Sabry saddlebrown Sadigh saed safezone Safran Sagui Saidi saip Salanne Salles sametag sandia Sandia sandybrown sanitizer Sanyal Sanz Sarath sc scafacos SCAFACOS scalability scalable Scalable scalexy scalexz scaleyz Scalfi Schaik Scheid Schilfgarde Schimansky Schiotz Schlitter Schmerler Schmid Schnieders Schoen Schotte Schratt Schulten Schunk Schuring Schwen Sci scp screenshot screenshots Scripps Scripta sd sdk sdpd SDPD se seagreen Searles Secor sectoring sed Seddon segmental Seibold Seifert Seleson sellerio Sellerio Semaev semiaxes semimetals Semin Sensable Seo Sep seqdep Serpico setfl setflag setforce Sethna setmask Setmask setpoint setvel sevenbody sfftw sfree sftp Sg sgcmc Shan Shanno Shapeev shapex shapey shapez shapshot shardlow Shardlow shawn Shen Shenderova Sherrill 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 Siochi Sirk Sival sixbody 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 sortfreq 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 stevens 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 suppressions 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 tabulary Tadmor Tafipolsky tagID tagint Tainter Tait taitwater Tajkhorshid Tamaskovics Tanaka tanh tanmoy Tanmoy Tartakovsky taskset taubi taup Tavenner taylor tb tchain Tchain Tcl Tcom tcsh tdamp tdpd tDPD Tdrude Technol Telsa tempCorrCoeff templated Templeton Tencer Tequil ters tersoff Tersoff tesselation tesselations Tetot tex textrm tfac tfmc tfMC tgnpt tgnvt th Thakkar Thakur 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 thr Threadripper threebody thrid ThunderX thylakoid THz Tieleman Tigran Tij Tildesley Timan timeflag timeI timespan timestamp timestamps timestep timestepping timesteps titlesec 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 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 triaxial 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 typestr Tz Tzou ub Uberuaga ubflag Ubflag ubiquitin uca uChem uCond uef UEF uf uf3 ufm Uhlenbeck Ui uind uInfParallel uinp uk ul ulb Uleft Ulomek uloop ulsph Ultrafast uMech Umbanhowar umin Umin un unary uncomment uncommented uncompress uncompute underdamped underprediction undump uniaxial uniaxially unicaen Unicaen unimodal uninstall unitarg unitless unittest Universite unix unmaintained unoptimized unordered unpadded unphysical unphysically unreacted 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Vsmall Vstream vstyle 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 wormlike wpbe wrapfig 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 xindy xk xlat xlattice 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 Yan Yanxon Yaser Yazdani Ybar ybox Yc yc ycm Yeh yellowgreen yEs Yethiraj yflag yhi yi ylat ylattice ylo ylz ymax ymin yml Yoshida ys ysc ysu yu Yu Yuh yukawa Yukawa Yusof Yuya yx yy yz Zagaceta Zannoni Zavada Zavattieri zbl ZBL Zc zc zcm zeeman Zeeman Zemer zenodo Zentrum Zepeda zerom zflag Zhang Zhao Zhen zhi Zhigilei Zhou Zhu zi Zi ziegenhain Ziegenhain zincblende zj Zj zlattice zlim zlo Zm zmax zmin zmq zN zs zsc Zsh zst Zstandard zstd Zstd zsu zu zx zy Zybin Zykova zz