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Improve C++-ness, eliminate some macros

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- fm_exp moved to math_special (exp2 was already there)
- use std::min/max template instead of macros
- use memory->create for dynamic arrays (still 1-indexed with macro)
- remove _ from function names, adjust method visibility
This commit is contained in:
Sebastian Hütter
2017-06-11 16:55:41 +02:00
parent fea28d8028
commit 9f852f5f58
12 changed files with 154 additions and 275 deletions
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135
src/USER-MEAMC/fm_exp.cpp
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@ -1,135 +0,0 @@
extern "C" {
/*
Copyright (c) 2012,2013 Axel Kohlmeyer <akohlmey@gmail.com>
All rights reserved.
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions
are met:
* Redistributions of source code must retain the above copyright
notice, this list of conditions and the following disclaimer.
* Redistributions in binary form must reproduce the above copyright
notice, this list of conditions and the following disclaimer in the
documentation and/or other materials provided with the distribution.
* Neither the name of the <organization> nor the
names of its contributors may be used to endorse or promote products
derived from this software without specific prior written permission.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
ARE DISCLAIMED. IN NO EVENT SHALL <COPYRIGHT HOLDER> BE LIABLE FOR ANY
DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF
THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
*/
/* faster versions of 2**x, e**x, and 10**x in single and double precision.
*
* Based on the Cephes math library 2.8
*/
#include <math.h>
#include <stdint.h>
/* internal definitions for the fastermath library */
/* IEEE 754 double precision floating point data manipulation */
typedef union
{
double f;
uint64_t u;
struct {int32_t i0,i1;};
} udi_t;
#define FM_DOUBLE_BIAS 1023
#define FM_DOUBLE_EMASK 2146435072
#define FM_DOUBLE_MBITS 20
#define FM_DOUBLE_MMASK 1048575
#define FM_DOUBLE_EZERO 1072693248
/* generate 2**num in floating point by bitshifting */
#define FM_DOUBLE_INIT_EXP(var,num) \
var.i0 = 0; \
var.i1 = (((int) num) + FM_DOUBLE_BIAS) << 20
/* double precision constants */
#define FM_DOUBLE_LOG2OFE 1.4426950408889634074
#define FM_DOUBLE_LOGEOF2 6.9314718055994530942e-1
#define FM_DOUBLE_LOG2OF10 3.32192809488736234789
#define FM_DOUBLE_LOG10OF2 3.0102999566398119521e-1
#define FM_DOUBLE_LOG10OFE 4.3429448190325182765e-1
#define FM_DOUBLE_SQRT2 1.41421356237309504880
#define FM_DOUBLE_SQRTH 0.70710678118654752440
/* optimizer friendly implementation of exp2(x).
*
* strategy:
*
* split argument into an integer part and a fraction:
* ipart = floor(x+0.5);
* fpart = x - ipart;
*
* compute exp2(ipart) from setting the ieee754 exponent
* compute exp2(fpart) using a pade' approximation for x in [-0.5;0.5[
*
* the result becomes: exp2(x) = exp2(ipart) * exp2(fpart)
*/
static const double fm_exp2_q[] = {
/* 1.00000000000000000000e0, */
2.33184211722314911771e2,
4.36821166879210612817e3
};
static const double fm_exp2_p[] = {
2.30933477057345225087e-2,
2.02020656693165307700e1,
1.51390680115615096133e3
};
static double fm_exp2(double x)
{
double ipart, fpart, px, qx;
udi_t epart;
ipart = floor(x+0.5);
fpart = x - ipart;
FM_DOUBLE_INIT_EXP(epart,ipart);
x = fpart*fpart;
px = fm_exp2_p[0];
px = px*x + fm_exp2_p[1];
qx = x + fm_exp2_q[0];
px = px*x + fm_exp2_p[2];
qx = qx*x + fm_exp2_q[1];
px = px * fpart;
x = 1.0 + 2.0*(px/(qx-px));
return epart.f*x;
}
double fm_exp(double x)
{
#if defined(__BYTE_ORDER__)
#if __BYTE_ORDER__ == __ORDER_LITTLE_ENDIAN__
return fm_exp2(FM_DOUBLE_LOG2OFE * x);
#endif
#endif
return exp(x);
}
/*
* Local Variables:
* mode: c
* compile-command: "make -C .."
* c-basic-offset: 4
* fill-column: 76
* indent-tabs-mode: nil
* End:
*/
}

60
src/USER-MEAMC/meam.h
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@ -2,31 +2,25 @@
#define LMP_MEAM_H #define LMP_MEAM_H
#include <stdlib.h> #include <stdlib.h>
#include "memory.h"
#define maxelt 5 #define maxelt 5
extern "C" {
double fm_exp(double);
}
namespace LAMMPS_NS { namespace LAMMPS_NS {
typedef enum { FCC, BCC, HCP, DIM, DIA, B1, C11, L12, B2 } lattice_t; typedef enum { FCC, BCC, HCP, DIM, DIA, B1, C11, L12, B2 } lattice_t;
struct allocatable_double_2d {
allocatable_double_2d() : dim1(0),dim2(0),ptr(0) {};
int dim1, dim2;
double* ptr;
};
class MEAM { class MEAM {
public: public:
MEAM(){}; MEAM(Memory *mem) :
memory(mem) {};
~MEAM() { ~MEAM() {
meam_cleanup_(); meam_cleanup();
} }
private: private:
Memory *&memory;
// cutforce = force cutoff // cutforce = force cutoff
// cutforcesq = force cutoff squared // cutforcesq = force cutoff squared
@ -89,10 +83,10 @@ class MEAM {
int eltind[maxelt + 1][maxelt + 1]; int eltind[maxelt + 1][maxelt + 1];
int neltypes; int neltypes;
allocatable_double_2d phir; // [:,:] double **phir;
allocatable_double_2d phirar, phirar1, phirar2, phirar3, phirar4, phirar5, double **phirar, **phirar1, **phirar2, **phirar3, **phirar4, **phirar5,
phirar6; // [:,:] **phirar6;
double attrac_meam[maxelt + 1][maxelt + 1], double attrac_meam[maxelt + 1][maxelt + 1],
repuls_meam[maxelt + 1][maxelt + 1]; repuls_meam[maxelt + 1][maxelt + 1];
@ -108,13 +102,10 @@ class MEAM {
int nr, nrar; int nr, nrar;
double dr, rdrar; double dr, rdrar;
public: protected:
void meam_checkindex(int, int, int, int*, int*); void meam_checkindex(int, int, int, int*, int*);
void meam_setup_param_(int*, double*, int*, int*, int*);
void meam_dens_final_(int*, int*, int*, int*, int*, double*, double*, int*, int*, int*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, int*);
void G_gam(double, int, double, double*, int*); void G_gam(double, int, double, double*, int*);
void dG_gam(double, int, double, double*, double*); void dG_gam(double, int, double, double*, double*);
void meam_dens_init_(int*, int*, int*, int*, int*, double*, int*, int*, int*, int*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, int*);
void getscreen(int, int, double*, double*, double*, double*, int, int*, int, int*, int, int*, int*); void getscreen(int, int, double*, double*, double*, double*, int, int*, int, int*, int, int*, int*);
void screen(int, int, int, double*, double, double*, int, int*, int, int*, int*); void screen(int, int, int, double*, double, double*, int, int*, int, int*, int*);
void calc_rho1(int, int, int, int*, int*, double*, int, int*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*); void calc_rho1(int, int, int, int*, int*, double*, int, int*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*);
@ -124,9 +115,6 @@ class MEAM {
void dCfunc(double, double, double, double*); void dCfunc(double, double, double, double*);
void dCfunc2(double, double, double, double*, double*); void dCfunc2(double, double, double, double*, double*);
void meam_force_(int*, int*, int*, int*, int*, int*, double*, double*, int*, int*, int*, double*, int*, int*, int*, int*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, int*);
void meam_cleanup_();
void meam_setup_done_(double*);
void alloyparams(); void alloyparams();
void compute_pair_meam(); void compute_pair_meam();
double phi_meam(double, int, int); double phi_meam(double, int, int);
@ -141,13 +129,17 @@ class MEAM {
double erose(double, double, double, double, double, double, int); double erose(double, double, double, double, double, double, int);
void interpolate_meam(int); void interpolate_meam(int);
double compute_phi(double, int, int); double compute_phi(double, int, int);
void meam_setup_global_(int*, int*, double*, int*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, int*); public:
void meam_setup_global(int*, int*, double*, int*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, int*);
void meam_setup_param(int*, double*, int*, int*, int*);
void meam_setup_done(double*);
void meam_dens_init(int*, int*, int*, int*, int*, double*, int*, int*, int*, int*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, int*);
void meam_dens_final(int*, int*, int*, int*, int*, double*, double*, int*, int*, int*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, int*);
void meam_force(int*, int*, int*, int*, int*, int*, double*, double*, int*, int*, int*, double*, int*, int*, int*, int*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, int*);
void meam_cleanup();
}; };
// Functions we need for compat // Functions we need for compat
#define MIN(A,B) ((A) < (B) ? (A) : (B))
#define MAX(A,B) ((A) > (B) ? (A) : (B))
#define iszero(f) (fabs(f) < 1e-20) #define iszero(f) (fabs(f) < 1e-20)
@ -171,7 +163,7 @@ Fortran Array Semantics in C.
- Multi-Dimensional MUST be declared in reverse, so that the order when accessing is the same as in Fortran - Multi-Dimensional MUST be declared in reverse, so that the order when accessing is the same as in Fortran
- arrays that are passed externally via the meam_* functions must use the arr*v() functions below - arrays that are passed externally via the meam_* functions must use the arr*v() functions below
(or be used with 0-based indexing) (or be used with 0-based indexing)
- allocatable arrays (only global phir*) are actually a struct, and must be accessed with arr2() - allocatable arrays must be accessed with arr2()
*/ */
// we receive a pointer to the first element, and F dimensions is ptr(a,b,c) // we receive a pointer to the first element, and F dimensions is ptr(a,b,c)
@ -194,19 +186,9 @@ Fortran Array Semantics in C.
ptr[(i - 1) + (j - 1) * (DIM1__##ptr) + \ ptr[(i - 1) + (j - 1) * (DIM1__##ptr) + \
(k - 1) * (DIM1__##ptr) * (DIM2__##ptr)] (k - 1) * (DIM1__##ptr) * (DIM2__##ptr)]
// allocatable arrays via special type // allocatable arrays
#define allocate_2d(arr, cols, rows) \
arr.dim1 = cols; \
arr.dim2 = rows; \
arr.ptr = (double*)calloc((size_t)(cols) * (size_t)(rows), sizeof(double));
#define allocated(a) (a.ptr != NULL)
#define meam_deallocate(a) \
({ \
free(a.ptr); \
a.ptr = NULL; \
})
// access data with same index as used in fortran (1-based) // access data with same index as used in fortran (1-based)
#define arr2(arr, i, j) arr.ptr[(arr.dim1) * (j - 1) + (i - 1)] #define arr2(arr, i, j) arr[j-1][i-1]
}; };

18
src/USER-MEAMC/meam_cleanup.cpp
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@ -3,15 +3,15 @@
using namespace LAMMPS_NS; using namespace LAMMPS_NS;
void void
MEAM::meam_cleanup_(void) MEAM::meam_cleanup(void)
{ {
meam_deallocate(this->phirar6); memory->destroy(this->phirar6);
meam_deallocate(this->phirar5); memory->destroy(this->phirar5);
meam_deallocate(this->phirar4); memory->destroy(this->phirar4);
meam_deallocate(this->phirar3); memory->destroy(this->phirar3);
meam_deallocate(this->phirar2); memory->destroy(this->phirar2);
meam_deallocate(this->phirar1); memory->destroy(this->phirar1);
meam_deallocate(this->phirar); memory->destroy(this->phirar);
meam_deallocate(this->phir); memory->destroy(this->phir);
} }

13
src/USER-MEAMC/meam_dens_final.cpp
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@ -1,5 +1,6 @@
#include "meam.h" #include "meam.h"
#include <math.h> #include <math.h>
#include "math_special.h"
using namespace LAMMPS_NS; using namespace LAMMPS_NS;
// Extern "C" declaration has the form: // Extern "C" declaration has the form:
@ -20,7 +21,7 @@ using namespace LAMMPS_NS;
// //
void void
MEAM::meam_dens_final_(int* nlocal, int* nmax, int* eflag_either, int* eflag_global, MEAM::meam_dens_final(int* nlocal, int* nmax, int* eflag_either, int* eflag_global,
int* eflag_atom, double* eng_vdwl, double* eatom, int* ntype, int* eflag_atom, double* eng_vdwl, double* eatom, int* ntype,
int* type, int* fmap, double* Arho1, double* Arho2, int* type, int* fmap, double* Arho1, double* Arho2,
double* Arho2b, double* Arho3, double* Arho3b, double* t_ave, double* Arho2b, double* Arho3, double* Arho3b, double* t_ave,
@ -221,7 +222,7 @@ MEAM::G_gam(double Gamma, int ibar, double gsmooth_factor, double* G, int* error
*G = sqrt(1.0 + Gamma); *G = sqrt(1.0 + Gamma);
} }
} else if (ibar == 1) { } else if (ibar == 1) {
*G = fm_exp(Gamma / 2.0); *G = MathSpecial::fm_exp(Gamma / 2.0);
} else if (ibar == 3) { } else if (ibar == 3) {
*G = 2.0 / (1.0 + exp(-Gamma)); *G = 2.0 / (1.0 + exp(-Gamma));
} else if (ibar == -5) { } else if (ibar == -5) {
@ -242,9 +243,9 @@ MEAM::dG_gam(double Gamma, int ibar, double gsmooth_factor, double* G, double* d
{ {
// Compute G(Gamma) and dG(gamma) based on selection flag ibar: // Compute G(Gamma) and dG(gamma) based on selection flag ibar:
// 0 => G = sqrt(1+Gamma) // 0 => G = sqrt(1+Gamma)
// 1 => G = fm_exp(Gamma/2) // 1 => G = MathSpecial::fm_exp(Gamma/2)
// 2 => not implemented // 2 => not implemented
// 3 => G = 2/(1+fm_exp(-Gamma)) // 3 => G = 2/(1+MathSpecial::fm_exp(-Gamma))
// 4 => G = sqrt(1+Gamma) // 4 => G = sqrt(1+Gamma)
// -5 => G = +-sqrt(abs(1+Gamma)) // -5 => G = +-sqrt(abs(1+Gamma))
double gsmooth_switchpoint; double gsmooth_switchpoint;
@ -264,10 +265,10 @@ MEAM::dG_gam(double Gamma, int ibar, double gsmooth_factor, double* G, double* d
*dG = 1.0 / (2.0 * *G); *dG = 1.0 / (2.0 * *G);
} }
} else if (ibar == 1) { } else if (ibar == 1) {
*G = fm_exp(Gamma / 2.0); *G = MathSpecial::fm_exp(Gamma / 2.0);
*dG = *G / 2.0; *dG = *G / 2.0;
} else if (ibar == 3) { } else if (ibar == 3) {
*G = 2.0 / (1.0 + fm_exp(-Gamma)); *G = 2.0 / (1.0 + MathSpecial::fm_exp(-Gamma));
*dG = *G * (2.0 - *G) / 2; *dG = *G * (2.0 - *G) / 2;
} else if (ibar == -5) { } else if (ibar == -5) {
if ((1.0 + Gamma) >= 0) { if ((1.0 + Gamma) >= 0) {

19
src/USER-MEAMC/meam_dens_init.cpp
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@ -1,5 +1,6 @@
#include "meam.h" #include "meam.h"
#include <math.h> #include <math.h>
#include "math_special.h"
using namespace LAMMPS_NS; using namespace LAMMPS_NS;
// Extern "C" declaration has the form: // Extern "C" declaration has the form:
@ -21,7 +22,7 @@ using namespace LAMMPS_NS;
// //
void void
MEAM::meam_dens_init_(int* i, int* nmax, int* ntype, int* type, int* fmap, double* x, MEAM::meam_dens_init(int* i, int* nmax, int* ntype, int* type, int* fmap, double* x,
int* numneigh, int* firstneigh, int* numneigh_full, int* numneigh, int* firstneigh, int* numneigh_full,
int* firstneigh_full, double* scrfcn, double* dscrfcn, int* firstneigh_full, double* scrfcn, double* dscrfcn,
double* fcpair, double* rho0, double* arho1, double* arho2, double* fcpair, double* rho0, double* arho1, double* arho2,
@ -209,14 +210,14 @@ MEAM::calc_rho1(int i, int nmax, int ntype, int* type, int* fmap, double* x,
aj = rij / this->re_meam[eltj][eltj] - 1.0; aj = rij / this->re_meam[eltj][eltj] - 1.0;
ro0i = this->rho0_meam[elti]; ro0i = this->rho0_meam[elti];
ro0j = this->rho0_meam[eltj]; ro0j = this->rho0_meam[eltj];
rhoa0j = ro0j * fm_exp(-this->beta0_meam[eltj] * aj) * sij; rhoa0j = ro0j * MathSpecial::fm_exp(-this->beta0_meam[eltj] * aj) * sij;
rhoa1j = ro0j * fm_exp(-this->beta1_meam[eltj] * aj) * sij; rhoa1j = ro0j * MathSpecial::fm_exp(-this->beta1_meam[eltj] * aj) * sij;
rhoa2j = ro0j * fm_exp(-this->beta2_meam[eltj] * aj) * sij; rhoa2j = ro0j * MathSpecial::fm_exp(-this->beta2_meam[eltj] * aj) * sij;
rhoa3j = ro0j * fm_exp(-this->beta3_meam[eltj] * aj) * sij; rhoa3j = ro0j * MathSpecial::fm_exp(-this->beta3_meam[eltj] * aj) * sij;
rhoa0i = ro0i * fm_exp(-this->beta0_meam[elti] * ai) * sij; rhoa0i = ro0i * MathSpecial::fm_exp(-this->beta0_meam[elti] * ai) * sij;
rhoa1i = ro0i * fm_exp(-this->beta1_meam[elti] * ai) * sij; rhoa1i = ro0i * MathSpecial::fm_exp(-this->beta1_meam[elti] * ai) * sij;
rhoa2i = ro0i * fm_exp(-this->beta2_meam[elti] * ai) * sij; rhoa2i = ro0i * MathSpecial::fm_exp(-this->beta2_meam[elti] * ai) * sij;
rhoa3i = ro0i * fm_exp(-this->beta3_meam[elti] * ai) * sij; rhoa3i = ro0i * MathSpecial::fm_exp(-this->beta3_meam[elti] * ai) * sij;
if (this->ialloy == 1) { if (this->ialloy == 1) {
rhoa1j = rhoa1j * this->t1_meam[eltj]; rhoa1j = rhoa1j * this->t1_meam[eltj];
rhoa2j = rhoa2j * this->t2_meam[eltj]; rhoa2j = rhoa2j * this->t2_meam[eltj];

24
src/USER-MEAMC/meam_force.cpp
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@ -1,5 +1,7 @@
#include "meam.h" #include "meam.h"
#include <math.h> #include <math.h>
#include <algorithm>
#include "math_special.h"
using namespace LAMMPS_NS; using namespace LAMMPS_NS;
// Extern "C" declaration has the form: // Extern "C" declaration has the form:
@ -24,7 +26,7 @@ using namespace LAMMPS_NS;
// //
void void
MEAM::meam_force_(int* iptr, int* nmax, int* eflag_either, int* eflag_global, MEAM::meam_force(int* iptr, int* nmax, int* eflag_either, int* eflag_global,
int* eflag_atom, int* vflag_atom, double* eng_vdwl, double* eatom, int* eflag_atom, int* vflag_atom, double* eng_vdwl, double* eatom,
int* ntype, int* type, int* fmap, double* x, int* numneigh, int* ntype, int* type, int* fmap, double* x, int* numneigh,
int* firstneigh, int* numneigh_full, int* firstneigh_full, int* firstneigh, int* numneigh_full, int* firstneigh_full,
@ -113,9 +115,9 @@ MEAM::meam_force_(int* iptr, int* nmax, int* eflag_either, int* eflag_global,
ind = this->eltind[elti][eltj]; ind = this->eltind[elti][eltj];
pp = rij * this->rdrar + 1.0; pp = rij * this->rdrar + 1.0;
kk = (int)pp; kk = (int)pp;
kk = MIN(kk, this->nrar - 1); kk = std::min(kk, this->nrar - 1);
pp = pp - kk; pp = pp - kk;
pp = MIN(pp, 1.0); pp = std::min(pp, 1.0);
phi = ((arr2(this->phirar3, kk, ind) * pp + phi = ((arr2(this->phirar3, kk, ind) * pp +
arr2(this->phirar2, kk, ind)) * arr2(this->phirar2, kk, ind)) *
pp + pp +
@ -144,26 +146,26 @@ MEAM::meam_force_(int* iptr, int* nmax, int* eflag_either, int* eflag_global,
invrei = 1.0 / this->re_meam[elti][elti]; invrei = 1.0 / this->re_meam[elti][elti];
ai = rij * invrei - 1.0; ai = rij * invrei - 1.0;
ro0i = this->rho0_meam[elti]; ro0i = this->rho0_meam[elti];
rhoa0i = ro0i * fm_exp(-this->beta0_meam[elti] * ai); rhoa0i = ro0i * MathSpecial::fm_exp(-this->beta0_meam[elti] * ai);
drhoa0i = -this->beta0_meam[elti] * invrei * rhoa0i; drhoa0i = -this->beta0_meam[elti] * invrei * rhoa0i;
rhoa1i = ro0i * fm_exp(-this->beta1_meam[elti] * ai); rhoa1i = ro0i * MathSpecial::fm_exp(-this->beta1_meam[elti] * ai);
drhoa1i = -this->beta1_meam[elti] * invrei * rhoa1i; drhoa1i = -this->beta1_meam[elti] * invrei * rhoa1i;
rhoa2i = ro0i * fm_exp(-this->beta2_meam[elti] * ai); rhoa2i = ro0i * MathSpecial::fm_exp(-this->beta2_meam[elti] * ai);
drhoa2i = -this->beta2_meam[elti] * invrei * rhoa2i; drhoa2i = -this->beta2_meam[elti] * invrei * rhoa2i;
rhoa3i = ro0i * fm_exp(-this->beta3_meam[elti] * ai); rhoa3i = ro0i * MathSpecial::fm_exp(-this->beta3_meam[elti] * ai);
drhoa3i = -this->beta3_meam[elti] * invrei * rhoa3i; drhoa3i = -this->beta3_meam[elti] * invrei * rhoa3i;
if (elti != eltj) { if (elti != eltj) {
invrej = 1.0 / this->re_meam[eltj][eltj]; invrej = 1.0 / this->re_meam[eltj][eltj];
aj = rij * invrej - 1.0; aj = rij * invrej - 1.0;
ro0j = this->rho0_meam[eltj]; ro0j = this->rho0_meam[eltj];
rhoa0j = ro0j * fm_exp(-this->beta0_meam[eltj] * aj); rhoa0j = ro0j * MathSpecial::fm_exp(-this->beta0_meam[eltj] * aj);
drhoa0j = -this->beta0_meam[eltj] * invrej * rhoa0j; drhoa0j = -this->beta0_meam[eltj] * invrej * rhoa0j;
rhoa1j = ro0j * fm_exp(-this->beta1_meam[eltj] * aj); rhoa1j = ro0j * MathSpecial::fm_exp(-this->beta1_meam[eltj] * aj);
drhoa1j = -this->beta1_meam[eltj] * invrej * rhoa1j; drhoa1j = -this->beta1_meam[eltj] * invrej * rhoa1j;
rhoa2j = ro0j * fm_exp(-this->beta2_meam[eltj] * aj); rhoa2j = ro0j * MathSpecial::fm_exp(-this->beta2_meam[eltj] * aj);
drhoa2j = -this->beta2_meam[eltj] * invrej * rhoa2j; drhoa2j = -this->beta2_meam[eltj] * invrej * rhoa2j;
rhoa3j = ro0j * fm_exp(-this->beta3_meam[eltj] * aj); rhoa3j = ro0j * MathSpecial::fm_exp(-this->beta3_meam[eltj] * aj);
drhoa3j = -this->beta3_meam[eltj] * invrej * rhoa3j; drhoa3j = -this->beta3_meam[eltj] * invrej * rhoa3j;
} else { } else {
rhoa0j = rhoa0i; rhoa0j = rhoa0i;

116
src/USER-MEAMC/meam_setup_done.cpp
View File

@ -1,5 +1,7 @@
#include "meam.h" #include "meam.h"
#include <math.h> #include <math.h>
#include <algorithm>
#include "math_special.h"
using namespace LAMMPS_NS; using namespace LAMMPS_NS;
// Declaration in pair_meam.h: // Declaration in pair_meam.h:
@ -12,7 +14,7 @@ using namespace LAMMPS_NS;
// //
void void
MEAM::meam_setup_done_(double* cutmax) MEAM::meam_setup_done(double* cutmax)
{ {
int nv2, nv3, m, n, p; int nv2, nv3, m, n, p;
@ -160,7 +162,7 @@ MEAM::alloyparams(void)
for (k = 1; k <= this->neltypes; k++) { for (k = 1; k <= this->neltypes; k++) {
eb = (this->Cmax_meam[i][j][k] * this->Cmax_meam[i][j][k]) / eb = (this->Cmax_meam[i][j][k] * this->Cmax_meam[i][j][k]) /
(4.0 * (this->Cmax_meam[i][j][k] - 1.0)); (4.0 * (this->Cmax_meam[i][j][k] - 1.0));
this->ebound_meam[i][j] = MAX(this->ebound_meam[i][j], eb); this->ebound_meam[i][j] = std::max(this->ebound_meam[i][j], eb);
} }
} }
} }
@ -183,43 +185,51 @@ MEAM::compute_pair_meam(void)
double C, s111, s112, s221, S11, S22; double C, s111, s112, s221, S11, S22;
// check for previously allocated arrays and free them // check for previously allocated arrays and free them
if (allocated(this->phir)) if (this->phir != NULL)
meam_deallocate(this->phir); memory->destroy(this->phir);
if (allocated(this->phirar)) if (this->phirar != NULL)
meam_deallocate(this->phirar); memory->destroy(this->phirar);
if (allocated(this->phirar1)) if (this->phirar1 != NULL)
meam_deallocate(this->phirar1); memory->destroy(this->phirar1);
if (allocated(this->phirar2)) if (this->phirar2 != NULL)
meam_deallocate(this->phirar2); memory->destroy(this->phirar2);
if (allocated(this->phirar3)) if (this->phirar3 != NULL)
meam_deallocate(this->phirar3); memory->destroy(this->phirar3);
if (allocated(this->phirar4)) if (this->phirar4 != NULL)
meam_deallocate(this->phirar4); memory->destroy(this->phirar4);
if (allocated(this->phirar5)) if (this->phirar5 != NULL)
meam_deallocate(this->phirar5); memory->destroy(this->phirar5);
if (allocated(this->phirar6)) if (this->phirar6 != NULL)
meam_deallocate(this->phirar6); memory->destroy(this->phirar6);
// allocate memory for array that defines the potential // allocate memory for array that defines the potential
allocate_2d(this->phir, this->nr, memory->create(this->phir, this->nr,
(this->neltypes * (this->neltypes + 1)) / 2); (this->neltypes * (this->neltypes + 1)) / 2,
"pair:phir");
// allocate coeff memory // allocate coeff memory
allocate_2d(this->phirar, this->nr, memory->create(this->phirar, this->nr,
(this->neltypes * (this->neltypes + 1)) / 2); (this->neltypes * (this->neltypes + 1)) / 2,
allocate_2d(this->phirar1, this->nr, "pair:phirar");
(this->neltypes * (this->neltypes + 1)) / 2); memory->create(this->phirar1, this->nr,
allocate_2d(this->phirar2, this->nr, (this->neltypes * (this->neltypes + 1)) / 2,
(this->neltypes * (this->neltypes + 1)) / 2); "pair:phirar1");
allocate_2d(this->phirar3, this->nr, memory->create(this->phirar2, this->nr,
(this->neltypes * (this->neltypes + 1)) / 2); (this->neltypes * (this->neltypes + 1)) / 2,
allocate_2d(this->phirar4, this->nr, "pair:phirar2");
(this->neltypes * (this->neltypes + 1)) / 2); memory->create(this->phirar3, this->nr,
allocate_2d(this->phirar5, this->nr, (this->neltypes * (this->neltypes + 1)) / 2,
(this->neltypes * (this->neltypes + 1)) / 2); "pair:phirar3");
allocate_2d(this->phirar6, this->nr, memory->create(this->phirar4, this->nr,
(this->neltypes * (this->neltypes + 1)) / 2); (this->neltypes * (this->neltypes + 1)) / 2,
"pair:phirar4");
memory->create(this->phirar5, this->nr,
(this->neltypes * (this->neltypes + 1)) / 2,
"pair:phirar5");
memory->create(this->phirar6, this->nr,
(this->neltypes * (this->neltypes + 1)) / 2,
"pair:phirar6");
// loop over pairs of element types // loop over pairs of element types
nv2 = 0; nv2 = 0;
@ -600,7 +610,7 @@ MEAM::compute_reference_density(void)
get_Zij2(&Z2, &arat, &scrn, this->lattce_meam[a][a], get_Zij2(&Z2, &arat, &scrn, this->lattce_meam[a][a],
this->Cmin_meam[a][a][a], this->Cmax_meam[a][a][a]); this->Cmin_meam[a][a][a], this->Cmax_meam[a][a][a]);
rho0_2nn = rho0_2nn =
this->rho0_meam[a] * fm_exp(-this->beta0_meam[a] * (arat - 1)); this->rho0_meam[a] * MathSpecial::fm_exp(-this->beta0_meam[a] * (arat - 1));
rho0 = rho0 + Z2 * rho0_2nn * scrn; rho0 = rho0 + Z2 * rho0_2nn * scrn;
} }
@ -667,8 +677,8 @@ MEAM::get_tavref(double* t11av, double* t21av, double* t31av, double* t12av,
} else { } else {
a1 = r / this->re_meam[a][a] - 1.0; a1 = r / this->re_meam[a][a] - 1.0;
a2 = r / this->re_meam[b][b] - 1.0; a2 = r / this->re_meam[b][b] - 1.0;
rhoa01 = this->rho0_meam[a] * fm_exp(-this->beta0_meam[a] * a1); rhoa01 = this->rho0_meam[a] * MathSpecial::fm_exp(-this->beta0_meam[a] * a1);
rhoa02 = this->rho0_meam[b] * fm_exp(-this->beta0_meam[b] * a2); rhoa02 = this->rho0_meam[b] * MathSpecial::fm_exp(-this->beta0_meam[b] * a2);
if (latt == L12) { if (latt == L12) {
rho01 = 8 * rhoa01 + 4 * rhoa02; rho01 = 8 * rhoa01 + 4 * rhoa02;
*t11av = (8 * t11 * rhoa01 + 4 * t12 * rhoa02) / rho01; *t11av = (8 * t11 * rhoa01 + 4 * t12 * rhoa02) / rho01;
@ -803,14 +813,14 @@ MEAM::get_densref(double r, int a, int b, double* rho01, double* rho11, double*
a1 = r / this->re_meam[a][a] - 1.0; a1 = r / this->re_meam[a][a] - 1.0;
a2 = r / this->re_meam[b][b] - 1.0; a2 = r / this->re_meam[b][b] - 1.0;
rhoa01 = this->rho0_meam[a] * fm_exp(-this->beta0_meam[a] * a1); rhoa01 = this->rho0_meam[a] * MathSpecial::fm_exp(-this->beta0_meam[a] * a1);
rhoa11 = this->rho0_meam[a] * fm_exp(-this->beta1_meam[a] * a1); rhoa11 = this->rho0_meam[a] * MathSpecial::fm_exp(-this->beta1_meam[a] * a1);
rhoa21 = this->rho0_meam[a] * fm_exp(-this->beta2_meam[a] * a1); rhoa21 = this->rho0_meam[a] * MathSpecial::fm_exp(-this->beta2_meam[a] * a1);
rhoa31 = this->rho0_meam[a] * fm_exp(-this->beta3_meam[a] * a1); rhoa31 = this->rho0_meam[a] * MathSpecial::fm_exp(-this->beta3_meam[a] * a1);
rhoa02 = this->rho0_meam[b] * fm_exp(-this->beta0_meam[b] * a2); rhoa02 = this->rho0_meam[b] * MathSpecial::fm_exp(-this->beta0_meam[b] * a2);
rhoa12 = this->rho0_meam[b] * fm_exp(-this->beta1_meam[b] * a2); rhoa12 = this->rho0_meam[b] * MathSpecial::fm_exp(-this->beta1_meam[b] * a2);
rhoa22 = this->rho0_meam[b] * fm_exp(-this->beta2_meam[b] * a2); rhoa22 = this->rho0_meam[b] * MathSpecial::fm_exp(-this->beta2_meam[b] * a2);
rhoa32 = this->rho0_meam[b] * fm_exp(-this->beta3_meam[b] * a2); rhoa32 = this->rho0_meam[b] * MathSpecial::fm_exp(-this->beta3_meam[b] * a2);
lat = this->lattce_meam[a][b]; lat = this->lattce_meam[a][b];
@ -889,8 +899,8 @@ MEAM::get_densref(double r, int a, int b, double* rho01, double* rho11, double*
a1 = arat * r / this->re_meam[a][a] - 1.0; a1 = arat * r / this->re_meam[a][a] - 1.0;
a2 = arat * r / this->re_meam[b][b] - 1.0; a2 = arat * r / this->re_meam[b][b] - 1.0;
rhoa01nn = this->rho0_meam[a] * fm_exp(-this->beta0_meam[a] * a1); rhoa01nn = this->rho0_meam[a] * MathSpecial::fm_exp(-this->beta0_meam[a] * a1);
rhoa02nn = this->rho0_meam[b] * fm_exp(-this->beta0_meam[b] * a2); rhoa02nn = this->rho0_meam[b] * MathSpecial::fm_exp(-this->beta0_meam[b] * a2);
if (lat == L12) { if (lat == L12) {
// As usual, L12 thinks it's special; we need to be careful computing // As usual, L12 thinks it's special; we need to be careful computing
@ -935,7 +945,7 @@ MEAM::zbl(double r, int z1, int z2)
double result = 0.0; double result = 0.0;
x = r / a; x = r / a;
for (i = 0; i <= 3; i++) { for (i = 0; i <= 3; i++) {
result = result + c[i] * fm_exp(-d[i] * x); result = result + c[i] * MathSpecial::fm_exp(-d[i] * x);
} }
if (r > 0.0) if (r > 0.0)
result = result * z1 * z2 / r * cc; result = result * z1 * z2 / r * cc;
@ -962,12 +972,12 @@ MEAM::erose(double r, double re, double alpha, double Ec, double repuls,
if (form == 1) if (form == 1)
result = -Ec * (1 + astar + (-attrac + repuls / r) * pow(astar, 3)) * result = -Ec * (1 + astar + (-attrac + repuls / r) * pow(astar, 3)) *
fm_exp(-astar); MathSpecial::fm_exp(-astar);
else if (form == 2) else if (form == 2)
result = -Ec * (1 + astar + a3 * pow(astar, 3)) * fm_exp(-astar); result = -Ec * (1 + astar + a3 * pow(astar, 3)) * MathSpecial::fm_exp(-astar);
else else
result = result =
-Ec * (1 + astar + a3 * pow(astar, 3) / (r / re)) * fm_exp(-astar); -Ec * (1 + astar + a3 * pow(astar, 3) / (r / re)) * MathSpecial::fm_exp(-astar);
} }
return result; return result;
} }
@ -1042,9 +1052,9 @@ MEAM::compute_phi(double rij, int elti, int eltj)
ind = this->eltind[elti][eltj]; ind = this->eltind[elti][eltj];
pp = rij * this->rdrar + 1.0; pp = rij * this->rdrar + 1.0;
kk = (int)pp; kk = (int)pp;
kk = MIN(kk, this->nrar - 1); kk = std::min(kk, this->nrar - 1);
pp = pp - kk; pp = pp - kk;
pp = MIN(pp, 1.0); pp = std::min(pp, 1.0);
double result = ((arr2(this->phirar3, kk, ind) * pp + double result = ((arr2(this->phirar3, kk, ind) * pp +
arr2(this->phirar2, kk, ind)) * arr2(this->phirar2, kk, ind)) *
pp + pp +

2
src/USER-MEAMC/meam_setup_global.cpp
View File

@ -18,7 +18,7 @@ using namespace LAMMPS_NS;
// //
void void
MEAM::meam_setup_global_(int* nelt, int* lat, double* z, int* ielement, double* atwt, MEAM::meam_setup_global(int* nelt, int* lat, double* z, int* ielement, double* atwt,
double* alpha, double* b0, double* b1, double* b2, double* alpha, double* b0, double* b1, double* b2,
double* b3, double* alat, double* esub, double* asub, double* b3, double* alat, double* esub, double* asub,
double* t0, double* t1, double* t2, double* t3, double* t0, double* t1, double* t2, double* t3,

11
src/USER-MEAMC/meam_setup_param.cpp
View File

@ -1,4 +1,5 @@
#include "meam.h" #include "meam.h"
#include <algorithm>
using namespace LAMMPS_NS; using namespace LAMMPS_NS;
// //
@ -58,7 +59,7 @@ MEAM::meam_checkindex(int num, int lim, int nidx, int* idx /*idx(3)*/, int* ierr
// 20 = bkgd_dyn // 20 = bkgd_dyn
void void
MEAM::meam_setup_param_(int* which_p, double* value_p, int* nindex_p, MEAM::meam_setup_param(int* which_p, double* value_p, int* nindex_p,
int* index /*index(3)*/, int* errorflag) int* index /*index(3)*/, int* errorflag)
{ {
//: index[0..2] //: index[0..2]
@ -149,8 +150,8 @@ MEAM::meam_setup_param_(int* which_p, double* value_p, int* nindex_p,
meam_checkindex(2, maxelt, nindex, index, errorflag); meam_checkindex(2, maxelt, nindex, index, errorflag);
if (*errorflag != 0) if (*errorflag != 0)
return; return;
i1 = MIN(index[0], index[1]); i1 = std::min(index[0], index[1]);
i2 = MAX(index[0], index[1]); i2 = std::max(index[0], index[1]);
this->nn2_meam[i1][i2] = (int)value; this->nn2_meam[i1][i2] = (int)value;
break; break;
@ -218,8 +219,8 @@ MEAM::meam_setup_param_(int* which_p, double* value_p, int* nindex_p,
meam_checkindex(2, maxelt, nindex, index, errorflag); meam_checkindex(2, maxelt, nindex, index, errorflag);
if (*errorflag != 0) if (*errorflag != 0)
return; return;
i1 = MIN(index[0], index[1]); i1 = std::min(index[0], index[1]);
i2 = MAX(index[0], index[1]); i2 = std::max(index[0], index[1]);
this->zbl_meam[i1][i2] = (int)value; this->zbl_meam[i1][i2] = (int)value;
break; break;

14
src/USER-MEAMC/pair_meamc.cpp
View File

@ -64,7 +64,7 @@ PairMEAMC::PairMEAMC(LAMMPS *lmp) : Pair(lmp)
nelements = 0; nelements = 0;
elements = NULL; elements = NULL;
mass = NULL; mass = NULL;
meam_inst = new MEAM; meam_inst = new MEAM(memory);
// set comm size needed by this Pair // set comm size needed by this Pair
@ -238,7 +238,7 @@ void PairMEAMC::compute(int eflag, int vflag)
for (ii = 0; ii < inum_half; ii++) { for (ii = 0; ii < inum_half; ii++) {
i = ilist_half[ii]; i = ilist_half[ii];
ifort = i+1; ifort = i+1;
meam_inst->meam_dens_init_(&ifort,&nmax,&ntype,type,fmap,&x[0][0], meam_inst->meam_dens_init(&ifort,&nmax,&ntype,type,fmap,&x[0][0],
&numneigh_half[i],firstneigh_half[i], &numneigh_half[i],firstneigh_half[i],
&numneigh_full[i],firstneigh_full[i], &numneigh_full[i],firstneigh_full[i],
&scrfcn[offset],&dscrfcn[offset],&fcpair[offset], &scrfcn[offset],&dscrfcn[offset],&fcpair[offset],
@ -255,7 +255,7 @@ void PairMEAMC::compute(int eflag, int vflag)
comm->reverse_comm_pair(this); comm->reverse_comm_pair(this);
meam_inst->meam_dens_final_(&nlocal,&nmax,&eflag_either,&eflag_global,&eflag_atom, meam_inst->meam_dens_final(&nlocal,&nmax,&eflag_either,&eflag_global,&eflag_atom,
&eng_vdwl,eatom,&ntype,type,fmap, &eng_vdwl,eatom,&ntype,type,fmap,
&arho1[0][0],&arho2[0][0],arho2b,&arho3[0][0], &arho1[0][0],&arho2[0][0],arho2b,&arho3[0][0],
&arho3b[0][0],&t_ave[0][0],&tsq_ave[0][0],gamma,dgamma1, &arho3b[0][0],&t_ave[0][0],&tsq_ave[0][0],gamma,dgamma1,
@ -280,7 +280,7 @@ void PairMEAMC::compute(int eflag, int vflag)
for (ii = 0; ii < inum_half; ii++) { for (ii = 0; ii < inum_half; ii++) {
i = ilist_half[ii]; i = ilist_half[ii];
ifort = i+1; ifort = i+1;
meam_inst->meam_force_(&ifort,&nmax,&eflag_either,&eflag_global,&eflag_atom, meam_inst->meam_force(&ifort,&nmax,&eflag_either,&eflag_global,&eflag_atom,
&vflag_atom,&eng_vdwl,eatom,&ntype,type,fmap,&x[0][0], &vflag_atom,&eng_vdwl,eatom,&ntype,type,fmap,&x[0][0],
&numneigh_half[i],firstneigh_half[i], &numneigh_half[i],firstneigh_half[i],
&numneigh_full[i],firstneigh_full[i], &numneigh_full[i],firstneigh_full[i],
@ -369,7 +369,7 @@ void PairMEAMC::coeff(int narg, char **arg)
// tell MEAM package that setup is done // tell MEAM package that setup is done
read_files(arg[2],arg[2+nelements+1]); read_files(arg[2],arg[2+nelements+1]);
meam_inst->meam_setup_done_(&cutmax); meam_inst->meam_setup_done(&cutmax);
// read args that map atom types to MEAM elements // read args that map atom types to MEAM elements
// map[i] = which element the Ith atom type is, -1 if not mapped // map[i] = which element the Ith atom type is, -1 if not mapped
@ -601,7 +601,7 @@ void PairMEAMC::read_files(char *globalfile, char *userfile)
// pass element parameters to MEAM package // pass element parameters to MEAM package
meam_inst->meam_setup_global_(&nelements,lat,z,ielement,atwt,alpha,b0,b1,b2,b3, meam_inst->meam_setup_global(&nelements,lat,z,ielement,atwt,alpha,b0,b1,b2,b3,
alat,esub,asub,t0,t1,t2,t3,rozero,ibar); alat,esub,asub,t0,t1,t2,t3,rozero,ibar);
// set element masses // set element masses
@ -717,7 +717,7 @@ void PairMEAMC::read_files(char *globalfile, char *userfile)
// pass single setting to MEAM package // pass single setting to MEAM package
int errorflag = 0; int errorflag = 0;
meam_inst->meam_setup_param_(&which,&value,&nindex,index,&errorflag); meam_inst->meam_setup_param(&which,&value,&nindex,index,&errorflag);
if (errorflag) { if (errorflag) {
char str[128]; char str[128];
sprintf(str,"MEAM library error %d",errorflag); sprintf(str,"MEAM library error %d",errorflag);

14
src/math_special.cpp
View File

@ -508,6 +508,9 @@ static const double fm_exp2_p[] = {
1.51390680115615096133e3 1.51390680115615096133e3
}; };
/* double precision constants */
#define FM_DOUBLE_LOG2OFE 1.4426950408889634074
double MathSpecial::exp2_x86(double x) double MathSpecial::exp2_x86(double x)
{ {
double ipart, fpart, px, qx; double ipart, fpart, px, qx;
@ -531,3 +534,14 @@ double MathSpecial::exp2_x86(double x)
x = 1.0 + 2.0*(px/(qx-px)); x = 1.0 + 2.0*(px/(qx-px));
return epart.f*x; return epart.f*x;
} }
double MathSpecial::fm_exp(double x)
{
#if defined(__BYTE_ORDER__)
#if __BYTE_ORDER__ == __ORDER_LITTLE_ENDIAN__
return exp2_x86(FM_DOUBLE_LOG2OFE * x);
#endif
#endif
return ::exp(x);
}

3
src/math_special.h
View File

@ -27,6 +27,9 @@ namespace MathSpecial {
// fast 2**x function without argument checks for little endian CPUs // fast 2**x function without argument checks for little endian CPUs
extern double exp2_x86(double x); extern double exp2_x86(double x);
// fast e**x function for little endian CPUs, falls back to libc on other platforms
extern double fm_exp(double x);
// scaled error function complement exp(x*x)*erfc(x) for coul/long styles // scaled error function complement exp(x*x)*erfc(x) for coul/long styles
static inline double my_erfcx(const double x) static inline double my_erfcx(const double x)