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Commit 7d9670bc authored by DallasTrinkle's avatar DallasTrinkle
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Addition of potential, code modifications to incorporate multicomponent spline... 

Addition of potential, code modifications to incorporate multicomponent spline MEAM in pair_meam_spline.

Backwards compatible with previous version of pair_meam_spline.
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potentials/TiO.meam.spline 0 → 100644
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View file @ 7d9670bc
# Ti-O cubic spline potential where O is in the dilute limit. DATE: 2016-06-05 CONTRIBUTOR: Pinchao Zhang, Dallas R. Trinkle
meam/spline 2 Ti O
spline3eq
13
-20 0
1.742692837 3.744277175966 99.4865081627958
2.05580176725 0.910839730906 10.8702523265355
2.3689106975 0.388045896634 -1.55322418749562
2.68201962775 -0.018840906533 2.43630041329215
2.995128558 -0.248098929639 2.67912713976835
3.30823748825 -0.264489550297 -0.125056384603077
3.6213464185 -0.227196189283 1.10662555360438
3.93445534875 -0.129293090176 -0.592053676745914
4.247564279 -0.059685366933 -0.470123414607672
4.56067320925 -0.031100025561 -0.0380739973059663
4.8737821395 -0.013847363202 -0.0711547960695406
5.18689106975 -0.003203412728 -0.081768292420175
5.5 0 -0.0571422964883619
spline3eq
5
0.155001355787331 0
1.9 0.533321679606674 0
2.8 0.456402081843862 -1.60311717015859
3.7 -0.324281383502201 1.19940299483249
4.6 -0.474029826906675 1.47909794595154
5.5 0 -2.49521499855605
spline3eq
13
0 0
1.742692837 0 0
2.05580176725 0 0
2.3689106975 0 0
2.68201962775 0 0
2.995128558 0 0
3.30823748825 0 0
3.6213464185 0 0
3.93445534875 0 0
4.247564279 0 0
4.56067320925 0 0
4.8737821395 0 0
5.18689106975 0 0
5.5 0 0
spline3eq
11
-1 0
2.055801767 1.7475279661 -525.869786904802
2.2912215903 -5.8677963945 252.796316927755
2.5266414136 -8.3376288737 71.7318388721015
2.7620612369 -5.8398712842 -1.93587742753693
2.9974810602 -3.1140648231 -39.2999192667503
3.2329008835 -1.7257245065 14.3424136002004
3.4683207068 -0.4428977017 -29.4925534559498
3.7037405301 -0.1466643003 -3.18010534572236
3.9391603534 -0.2095507945 3.33490838803603
4.1745801767 -0.1442384563 3.71918691359508
4.41 0 -9.66717019857564
spline3eq
5
-61.9827585211652 0
1.9 11.2293641315584 0
2.8 -27.9976343076148 122.648031332411
3.7 -8.32979773113248 -54.3340881766381
4.6 -1.00863195297399 3.23150064581724
5.5 0 -5.3514242228123
spline3eq
4
0.00776934946045395 0.105197706160344
-55.14233165 -0.29745568008 0.00152870603877451
-44.7409899033333 -0.15449458722 0.00038933722543571
-34.3396481566667 0.05098657168 0.00038124926922248
-23.93830641 0.57342694704 0.0156639264890892
spline3eq
5
-0.00676745157022662 -0.0159520381982146
-23.9928 0.297607384684645 0
-15.9241175 0.216691597077105 -0.0024248755353942
-7.855435 0.0637598673719069 0.00306245895013358
0.213247499999998 -0.00183450621970427 -0.00177588407633909
8.28193 -0.111277018874367 0
spline3eq
10
2.77327511656661 0
2.055801767 -0.1485215264 72.2010867146919
2.31737934844444 1.6845304918 -47.2744689053404
2.57895692988889 2.0113365977 -15.1859578405326
2.84053451133333 1.1444092747 3.33978204841873
3.10211209277778 0.2861606803 2.587867603808
3.36368967422222 -0.3459281126 6.14070694084556
3.62526725566667 -0.6257480601 3.7397696717154
3.88684483711111 -0.6119510826 4.64749084871402
4.14842241855556 -0.3112059651 2.83275746415936
4.41 0 -15.0612086827734
spline3eq
5
12.3315547862781 0
1.9 2.62105440156724 0
2.8 10.2850803058354 -25.439802988016
3.7 3.23933763743897 -7.20203673434025
4.6 -5.79049355858613 39.5509978688682
5.5 0 -41.221771373642
spline3eq
8
8.33642274810572 -60.4024574736564
-1 0.07651409193 -110.652321293778
-0.724509054371429 0.14155824541 44.8853405500508
-0.449018108742857 0.75788697341 -25.3065115342002
-0.173527163114286 0.63011570378 -2.48510144915082
0.101963782514286 0.09049597305 2.68769386908235
0.377454728142857 -0.35741586657 -1.01558570129633
0.652945673771428 -0.65293217647 13.4224786001212
0.9284366194 -6.00912190653 -452.752542694929
spline3eq
5
0.137191606537625 -1.55094230968985
-1 0.0513843442016519 0
-0.5 0.0179024412245673 -2.44986494990154
0 -0.260650876879273 3.91774583656401
0.5 -0.190163791764901 -4.84414871911743
1 -0.763795416646599 0
spline3eq
8
0 0
-1 0 0
-0.724509054371429 0 0
-0.449018108742857 0 0
-0.173527163114286 0 0
0.101963782514286 0 0
0.377454728142857 0 0
0.652945673771428 0 0
0.9284366194 0 0
src/USER-MISC/pair_meam_spline.cpp
+ 404
− 197
View file @ 7d9670bc
This diff is collapsed.
src/USER-MISC/pair_meam_spline.h
+ 34
− 16
View file @ 7d9670bc
/* -*- c++ -*- ----------------------------------------------------------
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
......@@ -43,10 +43,24 @@ public:
virtual void compute(int, int);
void settings(int, char **);
void coeff(int, char **);
void get_coeff(double *, double *);
double pair_density(int );
double three_body_density(int );
void init_style();
void init_list(int, class NeighList *);
double init_one(int, int);
// helper functions for compute()
double compute_three_body_contrib_to_charge_density(int i, int& numBonds); // returns rho_value and returns numBonds by reference
double compute_embedding_energy_and_deriv(int eflag, int i, double rho_value); // returns the derivative of the embedding energy Uprime_i
void compute_three_body_contrib_to_forces(int i, int numBonds, double Uprime_i);
void compute_two_body_pair_interactions();
int ij_to_potl(int i, int j);
int i_to_potl(int i);
int pack_forward_comm(int, int *, double *, int, int *);
void unpack_forward_comm(int, int, double *);
int pack_reverse_comm(int, int, double *);
......@@ -74,15 +88,15 @@ protected:
}
/// Initialization of spline function.
void init(int _n, double _deriv0, double _derivN) {
N = _n;
void init(int _N, double _deriv0, double _derivN) {
N = _N;
deriv0 = _deriv0;
derivN = _derivN;
delete[] X;
delete[] Xs;
delete[] Y;
delete[] Y2;
delete[] Ydelta;
// if (X) delete[] X;
// if (Xs) delete[] Xs;
// if (Y) delete[] Y;
// if (Y2) delete[] Y2;
// if (Ydelta) delete[] Ydelta;
X = new double[N];
Xs = new double[N];
Y = new double[N];
......@@ -97,7 +111,7 @@ protected:
int numKnots() const { return N; }
/// Parses the spline knots from a text file.
void parse(FILE* fp, Error* error);
void parse(FILE* fp, Error* error, bool isNewFormat);
/// Calculates the second derivatives of the cubic spline.
void prepareSpline(Error* error);
......@@ -209,18 +223,18 @@ protected:
/// Helper data structure for potential routine.
struct MEAM2Body {
int tag;
int tag; // holds the index of the second atom (j)
double r;
double f, fprime;
double del[3];
};
SplineFunction phi; // Phi(r_ij)
SplineFunction rho; // Rho(r_ij)
SplineFunction f; // f(r_ij)
SplineFunction U; // U(rho)
SplineFunction g; // g(cos_theta)
double zero_atom_energy; // Shift embedding energy by this value to make it zero for a single atom in vacuum.
SplineFunction* phis; // Phi_i(r_ij)
SplineFunction* rhos; // Rho_ij(r_ij)
SplineFunction* fs; // f_i(r_ij)
SplineFunction* Us; // U_i(rho)
SplineFunction* gs; // g_ij(cos_theta)
double* zero_atom_energies; // Shift embedding energy by this value to make it zero for a single atom in vacuum.
double cutoff; // The cutoff radius
......@@ -231,6 +245,8 @@ protected:
void read_file(const char* filename);
void allocate();
};
}
......@@ -279,3 +295,5 @@ protected:
*
* See file 'pair_spline_meam.cpp' for history of changes.
------------------------------------------------------------------------- */
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