From 8bce407ab5e2e8cd8fc4baeade0b3f600b8edc3a Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 3 Mar 2016 16:19:23 -0500 Subject: [PATCH] whitespace cleanup replaced all tabs with 8 spaces and deleted all trailing whitespace --- src/USER-MANIFOLD/fix_manifoldforce.cpp | 6 +- src/USER-MANIFOLD/fix_manifoldforce.h | 2 +- src/USER-MANIFOLD/fix_nve_manifold_rattle.cpp | 50 ++++++++--------- src/USER-MANIFOLD/fix_nve_manifold_rattle.h | 6 +- src/USER-MANIFOLD/fix_nvt_manifold_rattle.cpp | 36 ++++++------ src/USER-MANIFOLD/fix_nvt_manifold_rattle.h | 6 +- src/USER-MANIFOLD/manifold.h | 4 +- src/USER-MANIFOLD/manifold_dumbbell.cpp | 4 +- src/USER-MANIFOLD/manifold_ellipsoid.h | 4 +- src/USER-MANIFOLD/manifold_factory.cpp | 4 +- src/USER-MANIFOLD/manifold_factory.h | 2 +- src/USER-MANIFOLD/manifold_sphere.h | 8 +-- src/USER-MANIFOLD/manifold_spine.cpp | 4 +- src/USER-MANIFOLD/manifold_supersphere.h | 10 ++-- src/USER-MANIFOLD/manifold_thylakoid.cpp | 56 +++++++++---------- src/USER-MANIFOLD/manifold_thylakoid.h | 6 +- .../manifold_thylakoid_shared.cpp | 12 ++-- src/USER-MANIFOLD/manifold_thylakoid_shared.h | 4 +- 18 files changed, 112 insertions(+), 112 deletions(-) diff --git a/src/USER-MANIFOLD/fix_manifoldforce.cpp b/src/USER-MANIFOLD/fix_manifoldforce.cpp index 38754989a4..da794e4a48 100644 --- a/src/USER-MANIFOLD/fix_manifoldforce.cpp +++ b/src/USER-MANIFOLD/fix_manifoldforce.cpp @@ -57,7 +57,7 @@ FixManifoldForce::FixManifoldForce(LAMMPS *lmp, int narg, char **arg) : error->warning(FLERR,"Minimizing with fix manifoldforce without hftn or quickmin is fishy"); } - + // Command is given as // fix manifoldforce manifold_name manifold_args if( narg < 5 ){ @@ -65,7 +65,7 @@ FixManifoldForce::FixManifoldForce(LAMMPS *lmp, int narg, char **arg) : } const char *m_name = arg[3]; ptr_m = create_manifold(m_name,lmp,narg,arg); - + // Construct manifold from factory: if( !ptr_m ){ char msg[2048]; @@ -165,7 +165,7 @@ void FixManifoldForce::post_force(int vflag) f[i][0] -= dot*n[0] * invn2; f[i][1] -= dot*n[1] * invn2; f[i][2] -= dot*n[2] * invn2; - + } } } diff --git a/src/USER-MANIFOLD/fix_manifoldforce.h b/src/USER-MANIFOLD/fix_manifoldforce.h index 7c90ae7fbe..89bd6bd378 100644 --- a/src/USER-MANIFOLD/fix_manifoldforce.h +++ b/src/USER-MANIFOLD/fix_manifoldforce.h @@ -56,7 +56,7 @@ class FixManifoldForce : public Fix { void post_force(int); void post_force_respa(int, int, int); void min_post_force(int); - + private: user_manifold::manifold *ptr_m; diff --git a/src/USER-MANIFOLD/fix_nve_manifold_rattle.cpp b/src/USER-MANIFOLD/fix_nve_manifold_rattle.cpp index ea17937f99..d2d73de6bd 100644 --- a/src/USER-MANIFOLD/fix_nve_manifold_rattle.cpp +++ b/src/USER-MANIFOLD/fix_nve_manifold_rattle.cpp @@ -83,7 +83,7 @@ FixNVEManifoldRattle::FixNVEManifoldRattle( LAMMPS *lmp, int &narg, char **arg, { if( lmp->citeme) lmp->citeme->add(cite_fix_nve_manifold_rattle); if( narg < 6 ) error->all(FLERR, "Illegal fix nve/manifold/rattle command"); - + // Set all bits/settings: time_integrate = 1; dynamic_group_allow = 1; @@ -110,7 +110,7 @@ FixNVEManifoldRattle::FixNVEManifoldRattle( LAMMPS *lmp, int &narg, char **arg, if( !tstrs || !tvars || !tstyle || !is_var ){ error->all(FLERR, "Error creating manifold arg arrays"); } - + // Loop over manifold args: for( int i = 0; i < nvars; ++i ){ int len = 0, offset = 0; @@ -136,7 +136,7 @@ FixNVEManifoldRattle::FixNVEManifoldRattle( LAMMPS *lmp, int &narg, char **arg, } ptr_m->post_param_init(); - + // Loop over rest of args: int argi = 6 + nvars; while( argi < narg ){ @@ -144,14 +144,14 @@ FixNVEManifoldRattle::FixNVEManifoldRattle( LAMMPS *lmp, int &narg, char **arg, nevery = force->inumeric(FLERR,arg[argi+1]); argi += 2; }else if( error_on_unknown_keyword ){ - char msg[2048]; + char msg[2048]; sprintf(msg,"Error parsing arg \"%s\".\n", arg[argi]); error->all(FLERR, msg); }else{ argi += 1; } } - + } @@ -182,7 +182,7 @@ void FixNVEManifoldRattle::reset_dt() dtf = 0.5 * update->dt * force->ftm2v; - + } void FixNVEManifoldRattle::print_stats( const char *header ) @@ -241,7 +241,7 @@ int FixNVEManifoldRattle::setmask() mask |= INITIAL_INTEGRATE; mask |= FINAL_INTEGRATE; if( nevery > 0 ) mask |= END_OF_STEP; - + return mask; } @@ -266,7 +266,7 @@ void FixNVEManifoldRattle::update_var_params() stats.x_iters_per_atom = 0.0; stats.v_iters_per_atom = 0.0; } - + double **ptr_params = ptr_m->get_params(); for( int i = 0; i < nvars; ++i ){ if( is_var[i] ){ @@ -309,7 +309,7 @@ int FixNVEManifoldRattle::dof(int igroup) // centre of mass corrections: if( dofs <= 1 ) dofs = 0; stats.dofs_removed = dofs; - + return dofs; } @@ -371,11 +371,11 @@ void FixNVEManifoldRattle::nve_x_rattle(int igroup, int groupbit) int *mask = atom->mask; int nlocal = atom->nlocal; int natoms = 0; - + if (igroup == atom->firstgroup){ nlocal = atom->nfirst; } - + if (rmass) { for (int i = 0; i < nlocal; i++){ @@ -470,7 +470,7 @@ void FixNVEManifoldRattle::rattle_manifold_x(double *x, double *v, vo[0] = v[0]; vo[1] = v[1]; vo[2] = v[2]; - + xo[0] = x[0]; xo[1] = x[1]; xo[2] = x[2]; @@ -490,10 +490,10 @@ void FixNVEManifoldRattle::rattle_manifold_x(double *x, double *v, no_dt[2] = dtfm*no[2]; // Assume that no_nn is roughly constant during iteration: - + const double c_inv = 1.0 / c; - + while ( 1 ) { v[0] = vt[0] - l*no_dt[0]; v[1] = vt[1] - l*no_dt[1]; @@ -530,7 +530,7 @@ void FixNVEManifoldRattle::rattle_manifold_x(double *x, double *v, ++iters; if( (res < tolerance) || (iters >= max_iter) ) break; - + // Update nn and g. gg = ptr_m->g(x); ptr_m->n(x,nn); @@ -543,7 +543,7 @@ void FixNVEManifoldRattle::rattle_manifold_x(double *x, double *v, tagi, x[0], x[1], x[2], res, iters); error->one(FLERR,msg); } - + // "sync" x and v: v[0] = vt[0] - l*no_dt[0]; v[1] = vt[1] - l*no_dt[1]; @@ -564,7 +564,7 @@ void FixNVEManifoldRattle::rattle_manifold_v(double *v, double *f, v[i][0] += dtfm * f[i][0]; v[i][1] += dtfm * f[i][1]; v[i][2] += dtfm * f[i][2]; - + Now you add the rattle-like update: vold - vnew + dtfm * F + mu * n_new = 0 dot( vnew, n_new ) = 0 @@ -604,7 +604,7 @@ void FixNVEManifoldRattle::rattle_manifold_v(double *v, double *f, const double n_inv = 1.0 / nn2; const double c_inv = 1.0 / c; - + do{ R[0] = vt[0] - v[0] - l * no_dt[0]; R[1] = vt[1] - v[1] - l * no_dt[1]; @@ -613,28 +613,28 @@ void FixNVEManifoldRattle::rattle_manifold_v(double *v, double *f, // Analytic solution to system J*(dx,dy,dz,dl)^T = R nn_R = n[0]*R[0] + n[1]*R[1] + n[2]*R[2]; - + dv[3] = -nn_R - R[3]; dv[3] *= n_inv; dv[0] = -n[0]*dv[3] - R[0]; dv[1] = -n[1]*dv[3] - R[1]; dv[2] = -n[2]*dv[3] - R[2]; dv[3] *= c_inv; - + v[0] -= dv[0]; v[1] -= dv[1]; v[2] -= dv[2]; l -= dv[3]; - + res = infnorm<4>(R); ++iters; }while( (res > tolerance) && (iters < max_iter) ); if( iters >= max_iter && res >= tolerance ){ - char msg[2048]; - sprintf(msg,"Failed to constrain atom %d (x = (%f, %f, %f)! res = %e, iters = %d\n", - tagi, x[0], x[1], x[2], res, iters); - error->all(FLERR,msg); + char msg[2048]; + sprintf(msg,"Failed to constrain atom %d (x = (%f, %f, %f)! res = %e, iters = %d\n", + tagi, x[0], x[1], x[2], res, iters); + error->all(FLERR,msg); } stats.v_iters += iters; diff --git a/src/USER-MANIFOLD/fix_nve_manifold_rattle.h b/src/USER-MANIFOLD/fix_nve_manifold_rattle.h index 88126da687..4bd17ab899 100755 --- a/src/USER-MANIFOLD/fix_nve_manifold_rattle.h +++ b/src/USER-MANIFOLD/fix_nve_manifold_rattle.h @@ -64,7 +64,7 @@ namespace LAMMPS_NS { int dofs_removed; bigint last_out; }; - + FixNVEManifoldRattle(LAMMPS *, int &, char **, int = 1); virtual ~FixNVEManifoldRattle(); // All this stuff is interface, so you DO need to implement them. @@ -95,7 +95,7 @@ namespace LAMMPS_NS { statistics stats; int update_style; int nvars; - + user_manifold::manifold *ptr_m; @@ -124,7 +124,7 @@ Self-explanatory. Check the input script syntax and compare to the documentation for the command. You can use -echo screen as a command-line option when running LAMMPS to see the offending line. -E: There is no manifold named ... +E: There is no manifold named ... Self-explanatory. You requested a manifold whose name was not registered at the factory. diff --git a/src/USER-MANIFOLD/fix_nvt_manifold_rattle.cpp b/src/USER-MANIFOLD/fix_nvt_manifold_rattle.cpp index 0621f386be..3801508336 100644 --- a/src/USER-MANIFOLD/fix_nvt_manifold_rattle.cpp +++ b/src/USER-MANIFOLD/fix_nvt_manifold_rattle.cpp @@ -90,10 +90,10 @@ FixNVTManifoldRattle::FixNVTManifoldRattle(LAMMPS *lmp, int narg, char **arg, // Set all bits/settings: dof_flag = 1; dthalf = dt4 = dt8 = 0; - + t_start = t_stop = t_period = t_current = t_target = ke_target = 0.0; t_freq = drag = tdrag_factor = 0; - + boltz = force->boltz, nktv2p = force->nktv2p; tdof = 0; mtchain = 3; @@ -117,11 +117,11 @@ FixNVTManifoldRattle::FixNVTManifoldRattle(LAMMPS *lmp, int narg, char **arg, }else if( strcmp( arg[argi], "tchain" ) == 0 ){ if( argi+1 >= narg ) error->all(FLERR,"Keyword 'tchain' needs 1 argument"); - + mtchain = force->inumeric(FLERR, arg[argi+1]); argi += 2; }else if( error_on_unknown_keyword ){ - char msg[2048]; + char msg[2048]; sprintf(msg,"Error parsing arg \"%s\".\n", arg[argi]); error->all(FLERR, msg); }else{ @@ -148,7 +148,7 @@ FixNVTManifoldRattle::FixNVTManifoldRattle(LAMMPS *lmp, int narg, char **arg, newarg[1] = group->names[igroup]; newarg[2] = (char*) "temp"; - + modify->add_compute(3,newarg); delete [] newarg; int icompute = modify->find_compute(id_temp); @@ -159,7 +159,7 @@ FixNVTManifoldRattle::FixNVTManifoldRattle(LAMMPS *lmp, int narg, char **arg, temperature = modify->compute[icompute]; if( temperature->tempbias ) which = BIAS; else which = NOBIAS; - + // Set t_freq from t_period t_freq = 1.0 / t_period; @@ -174,8 +174,8 @@ FixNVTManifoldRattle::FixNVTManifoldRattle(LAMMPS *lmp, int narg, char **arg, for( int ich = 0; ich < mtchain; ++ich ){ eta[ich] = eta_dot[ich] = eta_dotdot[ich] = 0.0; } - - + + } /* ---------------------------------------------------------------------- */ @@ -201,7 +201,7 @@ int FixNVTManifoldRattle::setmask() mask |= INITIAL_INTEGRATE; mask |= FINAL_INTEGRATE; if( nevery > 0 ) mask |= END_OF_STEP; - + return mask; } @@ -241,9 +241,9 @@ void FixNVTManifoldRattle::setup(int vflag) for( int ich = 1; ich < mtchain; ++ich ){ eta_mass[ich] = boltz * t_target * inv_t_freq2; } - + for( int ich = 1; ich < mtchain; ++ich ){ - eta_dotdot[ich] = (eta_mass[ich-1]*eta_dot[ich-1]*eta_dot[ich-1] - + eta_dotdot[ich] = (eta_mass[ich-1]*eta_dot[ich-1]*eta_dot[ich-1] - boltz * t_target ) / eta_mass[ich]; } } @@ -252,7 +252,7 @@ void FixNVTManifoldRattle::compute_temp_target() { t_current = temperature->compute_scalar(); - tdof = temperature->dof; + tdof = temperature->dof; double delta = update->ntimestep - update->beginstep; if (delta != 0.0){ @@ -270,7 +270,7 @@ void FixNVTManifoldRattle::nhc_temp_integrate() // t_current = temperature->compute_scalar(); // tdof = temperature->dof; compute_temp_target(); - + double expfac, kecurrent = tdof * boltz * t_current; double inv_t_freq2 = 1.0 / (t_freq*t_freq); eta_mass[0] = tdof * boltz * t_target * inv_t_freq2; @@ -298,7 +298,7 @@ void FixNVTManifoldRattle::nhc_temp_integrate() eta_dot[0] *= tdrag_factor * expfac; factor_eta = exp(-dthalf*eta_dot[0]); - + if( factor_eta == 0 ){ char msg[2048]; sprintf(msg, "WTF, factor_eta is 0! dthalf = %f, eta_dot[0] = %f", @@ -344,7 +344,7 @@ void FixNVTManifoldRattle::nh_v_temp() - + if( which == NOBIAS ){ for( int i = 0; i < nlocal; ++i ){ if( mask[i] & groupbit ){ @@ -363,7 +363,7 @@ void FixNVTManifoldRattle::nh_v_temp() temperature->restore_bias(i,v[i]); } } - } + } } @@ -394,7 +394,7 @@ void FixNVTManifoldRattle::final_integrate() void FixNVTManifoldRattle::reset_dt() { FixNVEManifoldRattle::reset_dt(); - + dthalf = 0.5 * update->dt; dt4 = 0.25 * update->dt; dt8 = 0.125 * update->dt; @@ -410,6 +410,6 @@ double FixNVTManifoldRattle::memory_usage() { double bytes = FixNVEManifoldRattle::memory_usage(); bytes += (4*mtchain+1)*sizeof(double); - + return bytes; } diff --git a/src/USER-MANIFOLD/fix_nvt_manifold_rattle.h b/src/USER-MANIFOLD/fix_nvt_manifold_rattle.h index c4f3999bc5..a9d3e3122f 100644 --- a/src/USER-MANIFOLD/fix_nvt_manifold_rattle.h +++ b/src/USER-MANIFOLD/fix_nvt_manifold_rattle.h @@ -67,13 +67,13 @@ namespace LAMMPS_NS { virtual double memory_usage(); - + protected: void compute_temp_target(); void nhc_temp_integrate(); void nh_v_temp(); - + double dthalf, dt4, dt8; char *id_temp; @@ -107,7 +107,7 @@ Self-explanatory. Check the input script syntax and compare to the documentation for the command. You can use -echo screen as a command-line option when running LAMMPS to see the offending line. -E: There is no manifold named ... +E: There is no manifold named ... Self-explanatory. You requested a manifold whose name was not registered at the factory. diff --git a/src/USER-MANIFOLD/manifold.h b/src/USER-MANIFOLD/manifold.h index e81c9d5e8d..82a565af38 100644 --- a/src/USER-MANIFOLD/manifold.h +++ b/src/USER-MANIFOLD/manifold.h @@ -71,7 +71,7 @@ namespace user_manifold { protected: double *params; }; - + // Some utility functions that are templated, so I implement them @@ -90,7 +90,7 @@ namespace user_manifold { inline double dot( double *a, double *b ){ return a[0]*b[0] + a[1]*b[1] + a[2]*b[2]; } - + } // namespace LAMMPS_NS diff --git a/src/USER-MANIFOLD/manifold_dumbbell.cpp b/src/USER-MANIFOLD/manifold_dumbbell.cpp index c261bc20c4..ed1583ac9a 100644 --- a/src/USER-MANIFOLD/manifold_dumbbell.cpp +++ b/src/USER-MANIFOLD/manifold_dumbbell.cpp @@ -12,7 +12,7 @@ manifold_dumbbell::manifold_dumbbell( LAMMPS *lmp, int argc, char **argv ) : man /* * Equation for dumbbell is: - * + * * -x^2 - y^2 + (a^2 - (z/c)^2)*( 1 + A*sin(const(z) *z^2) )^4 * const(z) = (z < 0) ? B2 : B * params[4] = { a, A, B, c } @@ -37,7 +37,7 @@ void manifold_dumbbell::n( const double *x, double *nn ) nn[0] = -2.0*x[0]; nn[1] = -2.0*x[1]; nn[2] = 8.0*A*A*A*A*B*x[2]*(a*a-(x[2]*x[2]/(c*c)))*cos(B*x[2]*x[2]) * - pow(sin(B*x[2]*x[2]),3)-2*x[2]*(1+pow(A*sin(B*x[2]*x[2]),4))/(c*c); + pow(sin(B*x[2]*x[2]),3)-2*x[2]*(1+pow(A*sin(B*x[2]*x[2]),4))/(c*c); } diff --git a/src/USER-MANIFOLD/manifold_ellipsoid.h b/src/USER-MANIFOLD/manifold_ellipsoid.h index 1e135fcef8..e23dbec72a 100644 --- a/src/USER-MANIFOLD/manifold_ellipsoid.h +++ b/src/USER-MANIFOLD/manifold_ellipsoid.h @@ -18,8 +18,8 @@ namespace user_manifold { static const char* type(){ return "ellipsoid"; } virtual const char *id(){ return type(); } - static int expected_argc(){ return NPARAMS; } - virtual int nparams(){ return NPARAMS; } + static int expected_argc(){ return NPARAMS; } + virtual int nparams(){ return NPARAMS; } }; } diff --git a/src/USER-MANIFOLD/manifold_factory.cpp b/src/USER-MANIFOLD/manifold_factory.cpp index ac7f3789f6..cbdeb62976 100644 --- a/src/USER-MANIFOLD/manifold_factory.cpp +++ b/src/USER-MANIFOLD/manifold_factory.cpp @@ -65,8 +65,8 @@ manifold* LAMMPS_NS::user_manifold::create_manifold(const char *mname, make_manifold_if ( &man, mname, lmp, narg, arg ); make_manifold_if ( &man, mname, lmp, narg, arg ); make_manifold_if ( &man, mname, lmp, narg, arg ); - - + + return man; } diff --git a/src/USER-MANIFOLD/manifold_factory.h b/src/USER-MANIFOLD/manifold_factory.h index aa5f228f15..a2f21861eb 100644 --- a/src/USER-MANIFOLD/manifold_factory.h +++ b/src/USER-MANIFOLD/manifold_factory.h @@ -101,7 +101,7 @@ namespace user_manifold { manifold* create_manifold(const char *, LAMMPS *, int , char ** ); - + } // namespace user_manifold } // namespace LAMMPS_NS diff --git a/src/USER-MANIFOLD/manifold_sphere.h b/src/USER-MANIFOLD/manifold_sphere.h index 7c903828a9..5d4ae55fda 100644 --- a/src/USER-MANIFOLD/manifold_sphere.h +++ b/src/USER-MANIFOLD/manifold_sphere.h @@ -3,7 +3,7 @@ #include "manifold.h" -namespace LAMMPS_NS { +namespace LAMMPS_NS { namespace user_manifold { @@ -29,7 +29,7 @@ namespace user_manifold { nn[0] = 2*x[0]; nn[1] = 2*x[1]; nn[2] = 2*x[2]; - + return r2 - R*R; } @@ -39,7 +39,7 @@ namespace user_manifold { nn[1] = 2*x[1]; nn[2] = 2*x[2]; } - + virtual void H( double *x, double h[3][3] ) { h[0][1] = h[0][2] = h[1][0] = h[1][2] = h[2][0] = h[2][1] = 0.0; @@ -49,7 +49,7 @@ namespace user_manifold { static const char* type(){ return "sphere"; } virtual const char *id(){ return type(); } static int expected_argc(){ return NPARAMS; } - virtual int nparams(){ return NPARAMS; } + virtual int nparams(){ return NPARAMS; } }; } diff --git a/src/USER-MANIFOLD/manifold_spine.cpp b/src/USER-MANIFOLD/manifold_spine.cpp index 6734eecf27..68bcaa0cc1 100644 --- a/src/USER-MANIFOLD/manifold_spine.cpp +++ b/src/USER-MANIFOLD/manifold_spine.cpp @@ -11,7 +11,7 @@ manifold_spine::manifold_spine( LAMMPS *lmp, int argc, char **argv ) : manifold( /* * Equation for spine is: - * + * * -x^2 - y^2 + (a^2 - (z/c)^2)*( 1 + A*sin(const(z) *z^2) )^4 * const(z) = (z < 0) ? B2 : B * params[5] = { a, A, B, B2, c } @@ -43,7 +43,7 @@ void manifold_spine::n( const double *x, double *nn ) nn[0] = -2.0*x[0]; nn[1] = -2.0*x[1]; nn[2] = 8.0*A*A*A*A*B*x[2]*(a*a-(x[2]*x[2]/(c*c)))*cos(B*x[2]*x[2]) * - pow(sin(B*x[2]*x[2]),3)-2*x[2]*(1+pow(A*sin(B*x[2]*x[2]),4))/(c*c); + pow(sin(B*x[2]*x[2]),3)-2*x[2]*(1+pow(A*sin(B*x[2]*x[2]),4))/(c*c); }else{ nn[0] = -2.0*x[0]; nn[1] = -2.0*x[1]; diff --git a/src/USER-MANIFOLD/manifold_supersphere.h b/src/USER-MANIFOLD/manifold_supersphere.h index b6249f6f28..1d9c62d7a2 100644 --- a/src/USER-MANIFOLD/manifold_supersphere.h +++ b/src/USER-MANIFOLD/manifold_supersphere.h @@ -20,7 +20,7 @@ namespace user_manifold { { return (a > 0) - (a < 0); } - + virtual double g( const double *x ) { double R = params[0]; @@ -30,7 +30,7 @@ namespace user_manifold { double zz = fabs(x[2]); double rr = pow(xx,q) + pow(yy,q) + pow(zz,q); - + return rr - pow(R,q); } @@ -45,14 +45,14 @@ namespace user_manifold { nn[1] = q * my_sign(x[1])*pow(yy,q-1); nn[2] = q * my_sign(x[2])*pow(zz,q-1); } - + static const char* type(){ return "supersphere"; } virtual const char *id(){ return type(); } static int expected_argc(){ return NPARAMS; } - virtual int nparams(){ return NPARAMS; } + virtual int nparams(){ return NPARAMS; } }; } } -#endif +#endif diff --git a/src/USER-MANIFOLD/manifold_thylakoid.cpp b/src/USER-MANIFOLD/manifold_thylakoid.cpp index 14cadf9a9c..719a2d3281 100644 --- a/src/USER-MANIFOLD/manifold_thylakoid.cpp +++ b/src/USER-MANIFOLD/manifold_thylakoid.cpp @@ -119,7 +119,7 @@ void manifold_thylakoid::n( const double *x, double *n ) thyla_part *manifold_thylakoid::get_thyla_part( const double *x, int *err_flag, std::size_t *idx ) { - + for( std::size_t i = 0; i < parts.size(); ++i ){ thyla_part *p = parts[i]; if( is_in_domain(p,x) ){ @@ -146,8 +146,8 @@ void manifold_thylakoid::init_domains() "wB = %f and lB = %f! %f > %f\n", LT, wB, lB, wB + 2*lB, LT); error->one(FLERR,msg); } - - // Determine some constant coordinates: + + // Determine some constant coordinates: x0 = -( 0.5*LB + lB + lT + LT + lT + pad); y0 = -( 0.5*LT + lT + pad ); z0 = -15; @@ -168,7 +168,7 @@ void manifold_thylakoid::init_domains() char msg[2048]; sprintf(msg,"Thylakoid expects ylo of at most %f, but found %f", y0, domain->boxlo[1]); - error->one(FLERR,msg); + error->one(FLERR,msg); } #endif @@ -178,7 +178,7 @@ void manifold_thylakoid::init_domains() x1 = -x0; y1 = -y0; z1 = -z0; - + Lx = x1 - x0; Ly = y1 - y0; Lz = z1 - z0; @@ -204,7 +204,7 @@ void manifold_thylakoid::init_domains() // Create and add the manifold parts to the array. thyla_part *p; - + // Determine coordinates of domain boundaries and centres of "mass": thyla_part_geom cllb, cllt, clrb, clrt; // Left thylakoid cylinder parts @@ -216,9 +216,9 @@ void manifold_thylakoid::init_domains() thyla_part_geom bl, br, bc; // Bridge left, right connectors and cylinder. - - + + // The bridge is three parts. // 1. A connector between the right face of the left grana and a cylinder // 2. A connector between the left face of the right grana and a cylinder @@ -250,7 +250,7 @@ void manifold_thylakoid::init_domains() p = make_cyl_to_plane_part(bl.pt[0], rB, lB, -1, bl.pt); set_domain(p, bl.lo, bl.hi); parts.push_back(p); - + // 2.: br.pt[0] = 0.5*LB; br.pt[1] = 0; @@ -273,9 +273,9 @@ void manifold_thylakoid::init_domains() p = make_cyl_to_plane_part(br.pt[0], rB, lB, 1, br.pt); set_domain(p, br.lo, br.hi); parts.push_back(p); - - + + // 3.: // Cylinder in between: bc.pt[0] = 0; @@ -285,7 +285,7 @@ void manifold_thylakoid::init_domains() bc.lo[0] = bl.pt[0]; bc.lo[1] = -Reff; bc.lo[2] = -Reff; - + bc.hi[0] = br.pt[0]; bc.hi[1] = Reff; bc.hi[2] = Reff; @@ -298,7 +298,7 @@ void manifold_thylakoid::init_domains() bc.lo[0], bc.hi[0], bc.lo[1], bc.hi[1], bc.lo[2], bc.hi[2]); } #endif // MANIFOLD_THYLAKOID_DEBUG - + parts.push_back(p); @@ -312,17 +312,17 @@ void manifold_thylakoid::init_domains() cllb.hi[0] = cllb.pt[0]; cllb.hi[1] = cllb.pt[1]; cllb.hi[2] = z1; - + p = make_cyl_part(1,1,0,cllb.pt,lT); set_domain(p, cllb.lo, cllb.hi); parts.push_back(p); - + // left left top cylinder cllt = cllb; cllt.lo[1] = y1 - pad - lT; cllt.hi[1] = y1; cllt.pt[1] = cllb.pt[1] + LT; - + p = make_cyl_part(1,1,0,cllt.pt,lT); set_domain(p, cllt.lo, cllt.hi); parts.push_back(p); @@ -342,7 +342,7 @@ void manifold_thylakoid::init_domains() clrt.pt[1] += LT; clrt.lo[1] = y1 - pad - lT; clrt.hi[1] = y1; - + p = make_cyl_part(1,1,0,clrt.pt,lT); set_domain(p, clrt.lo, clrt.hi); parts.push_back(p); @@ -362,7 +362,7 @@ void manifold_thylakoid::init_domains() p = make_plane_part(1,0,0,pll.pt); set_domain(p, pll.lo, pll.hi); parts.push_back(p); - + // left bottom plane plb.pt[0] = x0 + pad + lT + 0.5*LT; plb.pt[1] = y0 + pad; @@ -373,17 +373,17 @@ void manifold_thylakoid::init_domains() plb.hi[0] = plb.lo[0] + LT; plb.hi[1] = plb.lo[1] + pad + lT; plb.hi[2] = z1; - + p = make_plane_part(0,1,0,plb.pt); set_domain(p, plb.lo, plb.hi); parts.push_back(p); - + // left top plane plt = plb; plt.lo[1] = cllb.pt[1] + LT; plt.hi[1] = y1; plt.pt[1] = y1 - pad; - + p = make_plane_part(0,1,0,plt.pt); set_domain(p, plt.lo, plt.hi); parts.push_back(p); @@ -436,7 +436,7 @@ void manifold_thylakoid::init_domains() parts.push_back(p); - + thyla_part_geom::mirror(thyla_part_geom::DIR_X, &prl , &pll ); p = make_plane_part(1,0,0,prl.pt); set_domain(p, prl.lo, prl.hi); @@ -503,7 +503,7 @@ void manifold_thylakoid::set_domain( thyla_part *p, const std::vector &l p->xlo = lo[0]; p->ylo = lo[1]; p->zlo = lo[2]; - + p->xhi = hi[0]; p->yhi = hi[1]; p->zhi = hi[2]; @@ -512,13 +512,13 @@ void manifold_thylakoid::set_domain( thyla_part *p, const std::vector &l int manifold_thylakoid::is_in_domain( thyla_part *part, const double *x ) { bool domain_ok = (x[0] >= part->xlo) && (x[0] <= part->xhi) && - (x[1] >= part->ylo) && (x[1] <= part->yhi) && - (x[2] >= part->zlo) && (x[2] <= part->zhi); + (x[1] >= part->ylo) && (x[1] <= part->yhi) && + (x[2] >= part->zlo) && (x[2] <= part->zhi); if( !domain_ok ) return false; // From here on out, domain is ok. - + if( part->type == thyla_part::THYLA_TYPE_CYL_TO_PLANE ){ double R0 = part->params[1]; @@ -528,8 +528,8 @@ int manifold_thylakoid::is_in_domain( thyla_part *part, const double *x ) double dist2 = y*y + z*z; double RR = R0+R; double RR2 = RR*RR; - - + + if( dist2 < RR2 ){ return true; }else{ diff --git a/src/USER-MANIFOLD/manifold_thylakoid.h b/src/USER-MANIFOLD/manifold_thylakoid.h index 9928791b0d..231525950d 100644 --- a/src/USER-MANIFOLD/manifold_thylakoid.h +++ b/src/USER-MANIFOLD/manifold_thylakoid.h @@ -17,16 +17,16 @@ namespace user_manifold { enum { NPARAMS = 3 }; manifold_thylakoid( LAMMPS *lmp, int, char ** ); virtual ~manifold_thylakoid(); - + virtual double g( const double *x ); virtual void n( const double *x, double *n ); static const char* type(){ return "thylakoid"; } virtual const char *id(){ return type(); } - static int expected_argc(){ return NPARAMS; } + static int expected_argc(){ return NPARAMS; } virtual int nparams(){ return NPARAMS; } - + virtual void post_param_init(); virtual void checkup(); // Some diagnostics... private: diff --git a/src/USER-MANIFOLD/manifold_thylakoid_shared.cpp b/src/USER-MANIFOLD/manifold_thylakoid_shared.cpp index dd107dcbc3..5ea3e5b556 100644 --- a/src/USER-MANIFOLD/manifold_thylakoid_shared.cpp +++ b/src/USER-MANIFOLD/manifold_thylakoid_shared.cpp @@ -60,7 +60,7 @@ thyla_part::thyla_part( int type, double *args, double xlo, double ylo, double z * * As params it takes X0, R0, R, and a sign that determines whether it is * "left" (args[3] < 0) or "right" (args[3] > 0). - * + * * The args are: X0, R0, R, x0, y0, z0, sign. */ params[0] = args[0]; @@ -114,7 +114,7 @@ double thyla_part::g(const double *x) double dx = x[0] - X0; double dy = x[1] - Y0; double dz = x[2] - Z0; - + return a*dx*dx + b*dy*dy + c*dz*dz - R*R; break; } @@ -122,7 +122,7 @@ double thyla_part::g(const double *x) double X0 = params[0]; double R0 = params[1]; double R = params[2]; - + // Determine the centre of the sphere. double dx = (x[0] - X0); double dyz = sqrt( x[1]*x[1] + x[2]*x[2] ); @@ -184,16 +184,16 @@ void thyla_part::n( const double *x, double *n ) double R0 = params[1]; double R = params[2]; double s = (params[6] > 0.0) ? 1.0 : -1.0; - + // Determine the centre of the sphere. double dx = s*(x[0] - X0); double ryz = sqrt( x[1]*x[1] + x[2]*x[2] ); // Maybe sign is important here... // Normalize g and n so that the normal is continuous: double norm = 1.0 / (2.0 * R); - + n[0] = s*2*dx*norm; - + double const_part = 1.0 - (R0 + R) / ryz; n[1] = 2*x[1]*const_part*norm; n[2] = 2*x[2]*const_part*norm; diff --git a/src/USER-MANIFOLD/manifold_thylakoid_shared.h b/src/USER-MANIFOLD/manifold_thylakoid_shared.h index f80ad96405..756f392bbb 100644 --- a/src/USER-MANIFOLD/manifold_thylakoid_shared.h +++ b/src/USER-MANIFOLD/manifold_thylakoid_shared.h @@ -34,7 +34,7 @@ namespace user_manifold { int err_flag; tagint a_id; - + double xlo, xhi, ylo, yhi, zlo, zhi; double x0, y0, z0; @@ -50,7 +50,7 @@ namespace user_manifold { enum DIRS { DIR_X, DIR_Y, DIR_Z }; static void mirror( unsigned int axis, thyla_part_geom *m, const thyla_part_geom *o ); - + }; // struct thyla_part_geom