From e28f93dca42c00a3e992f57b911f73a8312a0b4e Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 19 Jan 2024 00:03:13 -0500 Subject: [PATCH] programming style updates --- src/AMOEBA/amoeba_file.cpp | 16 ++--- src/BOCS/fix_bocs.cpp | 87 ++++++++++------------------ src/DPD-REACT/fix_rx.cpp | 4 +- src/DPD-REACT/pair_multi_lucy.cpp | 3 +- src/DPD-REACT/pair_multi_lucy_rx.cpp | 9 +-- src/PHONON/fix_phonon.cpp | 2 +- src/REACTION/fix_bond_react.cpp | 52 ++++++++--------- 7 files changed, 73 insertions(+), 100 deletions(-) diff --git a/src/AMOEBA/amoeba_file.cpp b/src/AMOEBA/amoeba_file.cpp index 99a8474a81..a48af86ffe 100644 --- a/src/AMOEBA/amoeba_file.cpp +++ b/src/AMOEBA/amoeba_file.cpp @@ -25,14 +25,14 @@ using namespace LAMMPS_NS; -enum{UNKNOWN,FFIELD,LITERATURE,ATOMTYPE,VDWL,VDWLPAIR,BSTRETCH,SBEND,ABEND, - PAULI,DISPERSION,UB,OUTPLANE,TORSION,PITORSION,ATOMMULT, - QPENETRATION,DIPPOLAR,QTRANSFER,END_OF_FILE}; -enum{ALLINGER,BUFFERED_14_7}; -enum{ARITHMETIC,GEOMETRIC,CUBIC_MEAN,R_MIN,SIGMA,DIAMETER,HARMONIC,HHG,W_H}; -enum{MUTUAL,OPT,TCG,DIRECT}; -enum{NOFRAME,ZONLY,ZTHENX,BISECTOR,ZBISECT,THREEFOLD}; -enum{GEAR,ASPC,LSQR}; +enum { UNKNOWN, FFIELD, LITERATURE, ATOMTYPE, VDWL, VDWLPAIR, BSTRETCH, SBEND, ABEND, + PAULI, DISPERSION, UB, OUTPLANE, TORSION, PITORSION, ATOMMULT, QPENETRATION, DIPPOLAR, + QTRANSFER, END_OF_FILE }; +enum { ALLINGER, BUFFERED_14_7 }; +enum { ARITHMETIC, GEOMETRIC, CUBIC_MEAN, R_MIN, SIGMA, DIAMETER, HARMONIC, HHG, W_H }; +enum { MUTUAL, OPT, TCG, DIRECT }; +enum { NOFRAME, ZONLY, ZTHENX, BISECTOR, ZBISECT, THREEFOLD }; +enum { GEAR, ASPC, LSQR }; static constexpr int MAXLINE = 65536; // crazy big for TORSION-TORSION section static constexpr int MAX_TYPE_PER_GROUP = 6; // max types per AMOEBA group diff --git a/src/BOCS/fix_bocs.cpp b/src/BOCS/fix_bocs.cpp index dbf053b407..8cf770a2b0 100644 --- a/src/BOCS/fix_bocs.cpp +++ b/src/BOCS/fix_bocs.cpp @@ -1,4 +1,3 @@ -// clang-format off /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories @@ -42,31 +41,30 @@ using namespace LAMMPS_NS; using namespace FixConst; static const char cite_user_bocs_package[] = - "BOCS package: doi:10.1021/acs.jpcb.7b09993\n\n" - "@Article{Dunn2018,\n" - " author = {N. J. H. Dunn and K. M. Lebold and M. R. {DeLyser} and\n" - " J. F. Rudzinski and W. G. Noid},\n" - " title = {{BOCS}: Bottom-Up Open-Source Coarse-Graining Software},\n" - " journal = {J.~Phys.\\ Chem.~B},\n" - " year = 2018,\n" - " volume = 122,\n" - " number = 13,\n" - " pages = {3363--3377}\n" - "}\n\n"; - - - -enum{NOBIAS,BIAS}; -enum{NONE,XYZ,XY,YZ,XZ}; -enum{ISO,ANISO,TRICLINIC}; + "BOCS package: doi:10.1021/acs.jpcb.7b09993\n\n" + "@Article{Dunn2018,\n" + " author = {N. J. H. Dunn and K. M. Lebold and M. R. {DeLyser} and\n" + " J. F. Rudzinski and W. G. Noid},\n" + " title = {{BOCS}: Bottom-Up Open-Source Coarse-Graining Software},\n" + " journal = {J.~Phys.\\ Chem.~B},\n" + " year = 2018,\n" + " volume = 122,\n" + " number = 13,\n" + " pages = {3363--3377}\n" + "}\n\n"; static constexpr double DELTAFLIP = 0.1; static constexpr double TILTMAX = 1.5; static constexpr int NUM_INPUT_DATA_COLUMNS = 2; // columns in the pressure correction file +enum { NOBIAS, BIAS }; +enum { NONE, XYZ, XY, YZ, XZ }; +enum { ISO, ANISO, TRICLINIC }; + /* ---------------------------------------------------------------------- NVT,NPH,NPT integrators for improved Nose-Hoover equations of motion ---------------------------------------------------------------------- */ +// clang-format off FixBocs::FixBocs(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg), id_dilate(nullptr), irregular(nullptr), id_temp(nullptr), @@ -75,7 +73,7 @@ FixBocs::FixBocs(LAMMPS *lmp, int narg, char **arg) : { if (lmp->citeme) lmp->citeme->add(cite_user_bocs_package); - if (narg < 4) error->all(FLERR,"Illegal fix bocs command"); + if (narg < 4) utils::missing_cmd_args(FLERR,"fix bocs",error); restart_global = 1; dynamic_group_allow = 1; @@ -649,17 +647,13 @@ int FixBocs::read_F_table( char *filename, int p_basis_type ) for (int i = 0; i < (int)inputLines.size(); ++i) { lineNum++; // count each line processed now so lineNum messages can be 1-based test_sscanf = sscanf(inputLines.at(i).c_str()," %f , %f ",&f1, &f2); - if (test_sscanf == 2) - { + if (test_sscanf == 2) { data[VOLUME][i] = (double)f1; data[PRESSURE_CORRECTION][i] = (double)f2; - if (i == 1) - { + if (i == 1) { // second entry is used to compute the validation interval used below stdVolumeInterval = data[VOLUME][i] - data[VOLUME][i-1]; - } - else if (i > 1) - { + } else if (i > 1) { // after second entry, all intervals are validated currVolumeInterval = data[VOLUME][i] - data[VOLUME][i-1]; if (fabs(currVolumeInterval - stdVolumeInterval) > volumeIntervalTolerance) { @@ -673,17 +667,14 @@ int FixBocs::read_F_table( char *filename, int p_basis_type ) } // no concluding else is intentional: i = 0, first line, no interval to validate } - } - else - { + } else { if (comm->me == 0) error->warning(FLERR,"Bad input format: did not find 2 comma separated numeric" " values in line {} of file {}\nWARNING:\tline: {}", lineNum, filename, inputLines.at(i)); badInput = true; } - if (badInput) - { + if (badInput) { numBadVolumeIntervals++; } } @@ -700,18 +691,13 @@ int FixBocs::read_F_table( char *filename, int p_basis_type ) error->warning(FLERR,"Bad volume / pressure-correction data: {}\nSee details above", filename); } - if (p_basis_type == BASIS_LINEAR_SPLINE) - { + if (p_basis_type == BASIS_LINEAR_SPLINE) { spline_length = numEntries; numEntries = build_linear_splines(data); - } - else if (p_basis_type == BASIS_CUBIC_SPLINE) - { + } else if (p_basis_type == BASIS_CUBIC_SPLINE) { spline_length = numEntries; numEntries = build_cubic_splines(data); - } - else - { + } else { error->all(FLERR,"ERROR: invalid p_basis_type value of {} in read_F_table", p_basis_type); } @@ -724,8 +710,7 @@ int FixBocs::build_linear_splines(double **data) { splines[VOLUME] = (double *) calloc(spline_length,sizeof(double)); splines[PRESSURE_CORRECTION] = (double *) calloc(spline_length,sizeof(double)); - for (int i = 0; i < spline_length; ++i) - { + for (int i = 0; i < spline_length; ++i) { splines[VOLUME][i] = data[VOLUME][i]; splines[PRESSURE_CORRECTION][i] = data[PRESSURE_CORRECTION][i]; } @@ -758,18 +743,15 @@ int FixBocs::build_cubic_splines(double **data) memory->create(mu, n, "mu"); memory->create(z, n, "z"); - for (int i=0; i1 && i<(n-1)) - { + if (i>1 && i<(n-1)) { alpha_i = (3.0 / h[i]) * ( data[1][i+1] - data[1][i]) - (3.0 / h[i-1] ) * ( data[1][i] - data[1][i-1] ); alpha[i-1] = alpha_i; @@ -779,8 +761,7 @@ int FixBocs::build_cubic_splines(double **data) mu[0] = 0.0; z[0] = 0.0; - for (int i=1; i=0; j--) - { + for (int j=n-1; j>=0; j--) { c[j] = z[j] - mu[j]*c[j+1]; - b[j] = (a[j+1]-a[j])/h[j] - h[j]*(c[j+1] + 2.0 * c[j])/3.0; - d[j] = (c[j+1]-c[j])/(3.0 * h[j]); } int numSplines = n - 1; memory->create(splines, NUM_CUBIC_SPLINE_COLUMNS, numSplines, "splines"); - for (int idx = 0; idx < numSplines; ++idx) - { + for (int idx = 0; idx < numSplines; ++idx) { splines[0][idx] = data[0][idx]; splines[1][idx] = a[idx]; splines[2][idx] = b[idx]; diff --git a/src/DPD-REACT/fix_rx.cpp b/src/DPD-REACT/fix_rx.cpp index 96f8ec6a7d..69eab4dbee 100644 --- a/src/DPD-REACT/fix_rx.cpp +++ b/src/DPD-REACT/fix_rx.cpp @@ -38,8 +38,8 @@ using namespace LAMMPS_NS; using namespace FixConst; using namespace MathSpecial; -enum{NONE,HARMONIC}; -enum{LUCY}; +enum { NONE, HARMONIC }; +enum { LUCY }; static constexpr int MAXLINE = 1024; static constexpr int DELTA = 4; diff --git a/src/DPD-REACT/pair_multi_lucy.cpp b/src/DPD-REACT/pair_multi_lucy.cpp index a51e7b551e..918246dcde 100644 --- a/src/DPD-REACT/pair_multi_lucy.cpp +++ b/src/DPD-REACT/pair_multi_lucy.cpp @@ -39,8 +39,7 @@ using namespace LAMMPS_NS; using MathConst::MY_PI; -enum{NONE,RLINEAR,RSQ}; - +enum { NONE, RLINEAR, RSQ }; static constexpr int MAXLINE = 1024; static const char cite_pair_multi_lucy[] = diff --git a/src/DPD-REACT/pair_multi_lucy_rx.cpp b/src/DPD-REACT/pair_multi_lucy_rx.cpp index 4b61bf3a4d..5ff03de6e7 100644 --- a/src/DPD-REACT/pair_multi_lucy_rx.cpp +++ b/src/DPD-REACT/pair_multi_lucy_rx.cpp @@ -41,7 +41,7 @@ using namespace LAMMPS_NS; using MathConst::MY_PI; -enum{NONE,RLINEAR,RSQ}; +enum{ NONE, RLINEAR, RSQ }; static constexpr int MAXLINE = 1024; @@ -488,11 +488,8 @@ void PairMultiLucyRX::read_table(Table *tb, char *file, char *keyword) // open file FILE *fp = utils::open_potential(file,lmp,nullptr); - if (fp == nullptr) { - char str[128]; - snprintf(str,128,"Cannot open file %s",file); - error->one(FLERR,str); - } + if (fp == nullptr) + error->one(FLERR, "Cannot open file {}: {}",file,utils::getsyserror()); // loop until section found with matching keyword diff --git a/src/PHONON/fix_phonon.cpp b/src/PHONON/fix_phonon.cpp index 9ed39bc861..786931a549 100644 --- a/src/PHONON/fix_phonon.cpp +++ b/src/PHONON/fix_phonon.cpp @@ -47,7 +47,7 @@ using namespace FixConst; static constexpr int MAXLINE = 512; -enum{FORWARD=-1,BACKWARD=1}; +enum{ FORWARD=-1, BACKWARD=1 }; static const char cite_fix_phonon[] = "fix phonon command: doi:10.1016/j.cpc.2011.04.019\n\n" diff --git a/src/REACTION/fix_bond_react.cpp b/src/REACTION/fix_bond_react.cpp index 34a5d3bcec..d8561b3959 100644 --- a/src/REACTION/fix_bond_react.cpp +++ b/src/REACTION/fix_bond_react.cpp @@ -1,4 +1,3 @@ -// clang-format off /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories @@ -58,26 +57,26 @@ using namespace FixConst; using namespace MathConst; static const char cite_fix_bond_react[] = - "fix bond/react: reacter.org doi:10.1016/j.polymer.2017.09.038, doi:10.1021/acs.macromol.0c02012\n\n" - "@Article{Gissinger17,\n" - " author = {J. R. Gissinger and B. D. Jensen and K. E. Wise},\n" - " title = {Modeling Chemical Reactions in Classical Molecular Dynamics Simulations},\n" - " journal = {Polymer},\n" - " year = 2017,\n" - " volume = 128,\n" - " pages = {211--217}\n" - "}\n\n" - "@Article{Gissinger20,\n" - " author = {J. R. Gissinger, B. D. Jensen, K. E. Wise},\n" - " title = {{REACTER}: A Heuristic Method for Reactive Molecular Dynamics},\n" - " journal = {Macromolecules},\n" - " year = 2020,\n" - " volume = 53,\n" - " number = 22,\n" - " pages = {9953--9961}\n" - "}\n\n"; - "fix bond/react: reacter.org doi:10.1016/j.polymer.2017.09.038, " + "doi:10.1021/acs.macromol.0c02012\n\n" + "@Article{Gissinger17,\n" + " author = {J. R. Gissinger and B. D. Jensen and K. E. Wise},\n" + " title = {Modeling Chemical Reactions in Classical Molecular Dynamics Simulations},\n" + " journal = {Polymer},\n" + " year = 2017,\n" + " volume = 128,\n" + " pages = {211--217}\n" + "}\n\n" + "@Article{Gissinger20,\n" + " author = {J. R. Gissinger, B. D. Jensen, K. E. Wise},\n" + " title = {{REACTER}: A Heuristic Method for Reactive Molecular Dynamics},\n" + " journal = {Macromolecules},\n" + " year = 2020,\n" + " volume = 53,\n" + " number = 22,\n" + " pages = {9953--9961}\n" + "}\n\n"; + static constexpr double BIG = 1.0e20; static constexpr int DELTA = 16; static constexpr int MAXGUESS = 20; // max # of guesses allowed by superimpose algorithm @@ -91,24 +90,25 @@ static constexpr int NUMVARVALS = 5; // max # of keyword values that have va // CONTINUE: a neighbor has been assigned, skip to next neighbor // GUESSFAIL: a guess has failed (if no more restore points, status = 'REJECT') // RESTORE: restore mode, load most recent restore point -enum{ACCEPT,REJECT,PROCEED,CONTINUE,GUESSFAIL,RESTORE}; +enum { ACCEPT, REJECT, PROCEED, CONTINUE, GUESSFAIL, RESTORE }; // types of available reaction constraints -enum{DISTANCE,ANGLE,DIHEDRAL,ARRHENIUS,RMSD,CUSTOM}; +enum { DISTANCE, ANGLE, DIHEDRAL, ARRHENIUS, RMSD, CUSTOM }; // ID type used by constraint -enum{ATOM,FRAG}; +enum { ATOM, FRAG }; // keyword values that accept variables as input -enum{NEVERY,RMIN,RMAX,PROB,NRATE}; +enum { NEVERY, RMIN, RMAX, PROB, NRATE }; // flag for one-proc vs shared reaction sites -enum{LOCAL,GLOBAL}; +enum { LOCAL, GLOBAL }; // values for molecule_keyword -enum{OFF,INTER,INTRA}; +enum { OFF, INTER, INTRA }; /* ---------------------------------------------------------------------- */ +// clang-format off FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)