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Add new setups for Copper melting with LJ and EAM

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Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
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Rafael Ravedutti 2021-11-30 01:33:55 +01:00
parent f7010113bf
commit bb21a885a1
14 changed files with 96831 additions and 21 deletions
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DATE: 2007-06-11 UNITS: metal CONTRIBUTOR: Stephen Foiles, foiles@sandia.gov CITATION: Foiles et al, Phys Rev B, 33, 7983 (1986) COMMENT: Cu functions (universal 3), SM Foiles et al, PRB, 33, 7983 (1986)
29 63.550 3.6150 FCC
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303
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Cu functions (universal 4) - JB Adams et al J. Mater. Res., 4(1), 102 (1989)
29 63.550 3.6150 FCC
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2.5806091153285706e+00 2.6505063508648590e+00 2.7110079545661563e+00 2.7621015568249447e+00 2.8038645637913220e+00
2.8364542979766156e+00 2.8600981973448825e+00 2.8750842333755031e+00 2.8817516761559574e+00 2.8804823057701157e+00
2.8716921439699092e+00 2.8558237581894161e+00 2.8333391711552594e+00 2.8047133934346959e+00 2.7704285829676252e+00
2.7309688247181469e+00 2.6868155147671331e+00 2.6384433262347358e+00 2.5863167291097398e+00 2.5308870321738226e+00
2.4725899125317596e+00 2.4118433966060167e+00 2.3490462556752334e+00 2.2845767789603002e+00 2.2187918877813502e+00
2.1520265552815943e+00 2.0845934975626363e+00 2.0167831036919637e+00 1.9488635738636404e+00 1.8810812369508270e+00
1.8136610207193371e+00 1.7468070500507196e+00 1.6807033505858371e+00 1.6155146372447149e+00 1.5513871690559142e+00
1.4884496536383409e+00 1.4268141864958608e+00 1.3665772120042590e+00 1.3078204945836447e+00 1.2506120900523854e+00
1.1950073085502879e+00 1.1410496616995687e+00 1.0887717878420631e+00 1.0381963502565981e+00 9.8933690422003551e-01
9.4219872964247031e-01 8.9677962677415124e-01 8.5307067316958651e-01 8.1105694069385592e-01 7.7071817188505065e-01
7.3202941544290212e-01 6.9496162100761794e-01 6.5948219372701189e-01 6.2555550939233484e-01 5.9314339115629977e-01
5.6220554903693554e-01 5.3269998356387660e-01 5.0458335504023211e-01 4.7781131998032222e-01 4.5233883634534777e-01
4.2812043923464138e-01 4.0511048870905242e-01 3.8326339142174781e-01 3.6253379771729577e-01 3.4287677583286325e-01
3.2424796479760154e-01 3.0660370758054967e-01 2.8990116598452254e-01 2.7409841872609064e-01 2.5915454407883409e-01
2.4502968839369110e-01 2.3168512174254197e-01 2.1908328186436687e-01 2.0718780752542632e-01 1.9596356233750800e-01
1.8537665001230508e-01 1.7539442196444632e-01 1.6598547811304609e-01 1.5711966166996927e-01 1.4876804864444715e-01
1.4090293273673637e-01 1.3349780623990259e-01 1.2652733751724909e-01 1.1996734557434463e-01 1.1379477219856060e-01
1.0798765209582406e-01 1.0252508141368288e-01 9.7387185001678311e-02 9.2555082724584015e-02 8.8010855111109620e-02
8.3737508589961873e-02 7.9718940536826377e-02 7.5939904329596963e-02 7.2385974585237101e-02 6.9043512729294765e-02
6.5899633029043336e-02 6.2942169202580001e-02 6.0159641699440547e-02 5.7541225732930634e-02 5.5076720130546430e-02
5.2756517056398833e-02 5.0571572648238083e-02 4.8513378601664936e-02 4.6573934725081756e-02 4.4745722480991068e-02
4.3021679522073253e-02 4.1395175224364866e-02 3.9859987214311721e-02 3.8410278881708670e-02 3.7040577866510604e-02
3.5745755503880039e-02 3.4521007208912380e-02 3.3361833779917971e-02 3.2264023597108116e-02 3.1223635691821294e-02
3.0236983660070216e-02 2.9300620393215571e-02 2.8411323597772320e-02 2.7566082075896281e-02 2.6762082737777249e-02
2.5996698317105604e-02 2.5267475760840985e-02 2.4572125264713973e-02 2.3908509926274246e-02 2.3274635987705516e-02
2.2668643641204911e-02 2.2088798370316409e-02 2.1533482801290083e-02 2.1001189039288493e-02 2.0490511464994254e-02
2.0000139967999431e-02 1.9528853594166895e-02 1.9075514584991349e-02 1.8639062787818239e-02 1.8218510416650235e-02
1.7812937144080498e-02 1.7421485505751177e-02 1.7043356599549031e-02 1.6677806062561751e-02 1.6324140309613155e-02
1.5981713017976018e-02 1.5649921843605585e-02 1.5328205354974755e-02 1.5016040171312250e-02 1.4712938292708366e-02
1.4418444610242331e-02 1.4132134584901757e-02 1.3853612084676337e-02 1.3582507369821917e-02 1.3318475216818060e-02
1.3061193172097418e-02 1.2810359927147186e-02 1.2565693807050415e-02 1.2326931365025051e-02 1.2093826075940506e-02
1.1866147122233661e-02 1.1643678266026136e-02 1.1426216801644407e-02 1.1213572583084475e-02 1.1005567121320226e-02
1.0802032746662471e-02 1.0602811831688208e-02 1.0407756070544782e-02 1.0216725810699157e-02 1.0029589433467268e-02
9.8462227798860602e-03 9.6665086187306404e-03 9.4903361536790021e-03 9.3176005668363371e-03 9.1482025960089031e-03
8.9820481433065535e-03 8.8190479128032462e-03 8.6591170751522117e-03 8.5021749571883021e-03 8.3481447546937537e-03
8.1969532666261724e-03 8.0485306492223962e-03 7.9028101885199598e-03 7.7597280899136256e-03 7.6192232834934315e-03
7.4812372439735375e-03 7.3457138241272979e-03 7.2125991007052359e-03 7.0818412319012813e-03 6.9533903254870300e-03
6.8271983168139705e-03 6.7032188559211503e-03 6.5814072030662141e-03 6.4617201320263939e-03 6.3441158405819764e-03
6.2285538676237207e-03 6.1149950163802147e-03 6.0034012832899109e-03 5.8937357920846312e-03 5.7859627326801166e-03
5.6800473044990030e-03 5.5759556638887986e-03 5.4736548753111791e-03 5.3731128660109428e-03 5.2742983838981461e-03
5.1771809583849582e-03 5.0817308639591330e-03 4.9879190862693046e-03 4.8957172905357560e-03 4.8050977921015592e-03
4.7160335289582467e-03 4.6284980360953021e-03 4.5424654215287241e-03 4.4579103438822931e-03 4.3748079913988880e-03
4.2931340622749670e-03 4.2128647462132407e-03 4.1339767071033873e-03 4.0564470667446839e-03 3.9802533895282599e-03
3.9053736680121076e-03 3.8317863093158128e-03 3.7594701222811860e-03 3.6884043053326127e-03 3.6185684349951674e-03
3.5499424550168301e-03 3.4825066660512660e-03 3.4162417158645347e-03 3.3511285900229004e-03 3.2871486030347646e-03
3.2242833899080170e-03 3.1625148980992668e-03 3.1018253798278661e-03 3.0421973847258310e-03 2.9836137528083811e-03
2.9260576077371064e-03 2.8695123503632708e-03 2.8139616525287708e-03 2.7593894511106498e-03 2.7057799422959966e-03
2.6531175760685227e-03 2.6013870509009052e-03 2.5505733086344240e-03 2.5006615295404683e-03 2.4516371275501436e-03
2.4034857456453340e-03 2.3561932514012535e-03 2.3097457326723414e-03 2.2641294934160616e-03 2.2193310496436136e-03
2.1753371254977782e-03 2.1321346494441173e-03 2.0897107505768314e-03 2.0480527550303662e-03 2.0071481824917164e-03
1.9669847428123305e-03 1.9275503327108034e-03 1.8888330325659355e-03 1.8508211032951805e-03 1.8135029833145980e-03
1.7768672855772646e-03 1.7409027946878666e-03 1.7055984640891586e-03 1.6709434133182904e-03 1.6369269253308227e-03
1.6035384438881917e-03 1.5707675710093030e-03 1.5386040644797400e-03 1.5070378354209296e-03 1.4760589459142243e-03
1.4456576066784674e-03 1.4158241748004133e-03 1.3865491515145517e-03 1.3578231800324136e-03 1.3296370434173130e-03
1.3019816625059188e-03 1.2748480938728074e-03 1.2482275278369870e-03 1.2221112865106742e-03 1.1964908218862064e-03
1.1713577139624703e-03 1.1467036689077198e-03 1.1225205172586891e-03 1.0988002121543120e-03 1.0755348276031765e-03
1.0527165567835728e-03 1.0303377103750150e-03 1.0083907149206553e-03 9.8686811121878604e-04 9.6576255274356815e-04
9.4506680409354657e-04 9.2477373946662708e-04 9.0487634116191706e-04 8.8536769810608137e-04 8.6624100440530968e-04
8.4748955791986991e-04 8.2910675886310736e-04 8.1108610842155551e-04 7.9342120739794852e-04 7.7610575487466887e-04
7.5913354689786591e-04 7.4249847518158968e-04 7.2619452583109687e-04 7.1021577808524222e-04 6.9455640307671332e-04
6.7921066261025093e-04 6.6417290795844214e-04 6.4943757867335500e-04 6.3499920141575628e-04 6.2085238879914031e-04
6.0699183824991856e-04 5.9341233088238896e-04 5.8010873038847818e-04 5.6707598194186137e-04 5.5430911111587280e-04
5.4180322281523891e-04 5.2955350022104025e-04 5.1755520374872563e-04 5.0580367001857793e-04 4.9429431083891986e-04
4.8302261220136561e-04 4.7198413328763435e-04 4.6117450548847222e-04 4.5058943143359842e-04 4.4022468403297037e-04
4.3007610552883886e-04 4.2013960655883260e-04 4.1041116522908330e-04 4.0088682619821882e-04 3.9156269977118005e-04
3.8243496100300207e-04 3.7349984881274514e-04 3.6475366510662147e-04 3.5619277391102898e-04 3.4781360051482253e-04
3.3961263062063513e-04 3.3158640950565685e-04 3.2373154119109092e-04 3.1604468762060252e-04 3.0852256784754707e-04
3.0116195723081836e-04 2.9395968663908575e-04 2.8691264166377101e-04 2.8001776184017647e-04 2.7327203987681688e-04
2.6667252089326854e-04 2.6021630166557681e-04 2.5390052988028163e-04 2.4772240339593181e-04 2.4167916951265550e-04
2.3576812424967210e-04 2.2998661163024531e-04 2.2433202297460642e-04 2.1880179620031078e-04 2.1339341513026532e-04
2.0810440880823181e-04 2.0293235082175821e-04 1.9787485863260665e-04 1.9292959291436311e-04 1.8809425689761319e-04
1.8336659572205580e-04 1.7874439579616125e-04 1.7422548416372047e-04 1.6980772787763936e-04 1.6548903338088530e-04
1.6126734589430591e-04 1.5714064881157744e-04 1.5310696310104604e-04 1.4916434671449329e-04 1.4531089400280153e-04
1.4154473513841234e-04 1.3786403554466153e-04 1.3426699533172857e-04 1.3075184873951283e-04 1.2731686358694039e-04
1.2396034072819674e-04 1.2068061351527565e-04 1.1747604726729168e-04 1.1434503874632306e-04 1.1128601563955686e-04
1.0829743604811193e-04 1.0537778798212988e-04 1.0252558886227753e-04 9.9739385027582898e-05 9.7017751249615057e-05
9.4359290252773662e-05 9.1762632240957511e-05 8.9226434430383569e-05 8.6749380588361721e-05 8.4330180578390864e-05
8.1967569911181246e-05 7.9660309301724484e-05 7.7407184232279429e-05 7.5207004521348451e-05 7.3058603898526649e-05
7.0960839585107720e-05 6.8912591880629977e-05 6.6912763755002085e-05 6.4960280446513426e-05 6.3054089065330086e-05
6.1193158202771814e-05 5.9376477546041213e-05 5.7603057498502742e-05 5.5871928805544500e-05 5.4182142185708361e-05
5.2532767967318744e-05 5.0922895730446966e-05 4.9351633954125953e-05 4.7818109668823321e-05 4.6321468114150300e-05
4.4860872401664663e-05 4.3435503182825573e-05 4.2044558321957873e-05 4.0687252574273750e-05 3.9362817268785450e-05
3.8070499996214428e-05 3.6809564301621984e-05 3.5579289382025496e-05 3.4378969788611451e-05 3.3207915133769052e-05
3.2065449802711312e-05 3.0950912669766876e-05 2.9863656819185611e-05 2.8803049270468119e-05 2.7768470708167169e-05
2.6759315216115260e-05 2.5774990015931323e-05 2.4814915209964844e-05 2.3878523528387922e-05 2.2965260080560611e-05
2.2074582110528148e-05 2.1205958756658535e-05 2.0358870815317476e-05 1.9532810508535560e-05 1.8727281255713447e-05
1.7941797449145505e-05 1.7175884233475961e-05 1.6429077288930018e-05 1.5700922618341645e-05 1.4990976337865471e-05
1.4298804471386687e-05 1.3623982748522034e-05 1.2966096406226424e-05 1.2324739993882115e-05 1.1699517181902770e-05
1.1090040573734860e-05 1.0495931521266495e-05 9.9168199435395021e-06 9.3523441487842465e-06 8.8021506596591475e-06
8.2658940417265321e-06 7.7432367350197678e-06 7.2338488887770244e-06 6.7374081991923703e-06 6.2535997501888662e-06
5.7821158571569505e-06 5.3226559136389283e-06 4.8749262408651290e-06 4.4386399401326240e-06 4.0135167480073166e-06
3.5992828942305738e-06 3.1956709623667747e-06 2.8024197531120341e-06 2.4192741502208947e-06 2.0459849890155880e-06
1.6823089274468580e-06 1.3280083196495871e-06 9.8285109196557868e-07 6.4661062138351467e-07 3.1906561636122974e-07
0. 0. 0. 0. 0.

32009
data/input_eam_cu_one_atomtype_20x20x20.dmp Normal file
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32009
data/input_lj_cu_one_atomtype_20x20x20.dmp Normal file
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32009
data/input_lj_cu_two_atomtypes_20x20x20.dmp Normal file
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102
src/atom.c
View File

@ -24,6 +24,7 @@
*/ */
#include <stdlib.h> #include <stdlib.h>
#include <stdio.h> #include <stdio.h>
#include <string.h>
#include <math.h> #include <math.h>
#include <atom.h> #include <atom.h>
@ -32,6 +33,14 @@
#define DELTA 20000 #define DELTA 20000
#ifndef MAXLINE
#define MAXLINE 4096
#endif
#ifndef MAX
#define MAX(a,b) ((a) > (b) ? (a) : (b))
#endif
void initAtom(Atom *atom) void initAtom(Atom *atom)
{ {
atom->x = NULL; atom->y = NULL; atom->z = NULL; atom->x = NULL; atom->y = NULL; atom->z = NULL;
@ -152,6 +161,99 @@ void createAtom(Atom *atom, Parameter *param)
} }
} }
int readAtom(Atom* atom, Parameter* param)
{
FILE *fp = fopen(param->input_file, "r");
char line[MAXLINE];
int natoms = 0;
int read_atoms = 0;
int atom_id = -1;
int ts = -1;
if(!fp) {
fprintf(stderr, "Could not open input file: %s\n", param->input_file);
exit(-1);
return -1;
}
while(!feof(fp) && ts < 1 && !read_atoms) {
fgets(line, MAXLINE, fp);
if(strncmp(line, "ITEM: ", 6) == 0) {
char *item = &line[6];
if(strncmp(item, "TIMESTEP", 8) == 0) {
fgets(line, MAXLINE, fp);
ts = atoi(line);
} else if(strncmp(item, "NUMBER OF ATOMS", 15) == 0) {
fgets(line, MAXLINE, fp);
natoms = atoi(line);
atom->Natoms = natoms;
atom->Nlocal = natoms;
while(atom->Nlocal >= atom->Nmax) {
growAtom(atom);
}
} else if(strncmp(item, "BOX BOUNDS pp pp pp", 19) == 0) {
fgets(line, MAXLINE, fp);
param->xlo = atof(strtok(line, " "));
param->xhi = atof(strtok(NULL, " "));
param->xprd = param->xhi - param->xlo;
fgets(line, MAXLINE, fp);
param->ylo = atof(strtok(line, " "));
param->yhi = atof(strtok(NULL, " "));
param->yprd = param->yhi - param->ylo;
fgets(line, MAXLINE, fp);
param->zlo = atof(strtok(line, " "));
param->zhi = atof(strtok(NULL, " "));
param->zprd = param->zhi - param->zlo;
} else if(strncmp(item, "ATOMS id type x y z vx vy vz", 28) == 0) {
for(int i = 0; i < natoms; i++) {
fgets(line, MAXLINE, fp);
atom_id = atoi(strtok(line, " ")) - 1;
atom->type[atom_id] = atoi(strtok(NULL, " "));
atom_x(atom_id) = atof(strtok(NULL, " "));
atom_y(atom_id) = atof(strtok(NULL, " "));
atom_z(atom_id) = atof(strtok(NULL, " "));
atom->vx[atom_id] = atof(strtok(NULL, " "));
atom->vy[atom_id] = atof(strtok(NULL, " "));
atom->vz[atom_id] = atof(strtok(NULL, " "));
atom->ntypes = MAX(atom->type[atom_id], atom->ntypes);
read_atoms++;
}
} else {
fprintf(stderr, "Invalid item: %s\n", item);
exit(-1);
return -1;
}
} else {
fprintf(stderr, "Invalid input from file, expected item reference but got:\n%s\n", line);
exit(-1);
return -1;
}
}
if(ts < 0 || !natoms || !read_atoms) {
fprintf(stderr, "Input error: atom data was not read!\n");
exit(-1);
return -1;
}
atom->epsilon = allocate(ALIGNMENT, atom->ntypes * atom->ntypes * sizeof(MD_FLOAT));
atom->sigma6 = allocate(ALIGNMENT, atom->ntypes * atom->ntypes * sizeof(MD_FLOAT));
atom->cutforcesq = allocate(ALIGNMENT, atom->ntypes * atom->ntypes * sizeof(MD_FLOAT));
atom->cutneighsq = allocate(ALIGNMENT, atom->ntypes * atom->ntypes * sizeof(MD_FLOAT));
for(int i = 0; i < atom->ntypes * atom->ntypes; i++) {
atom->epsilon[i] = param->epsilon;
atom->sigma6[i] = param->sigma6;
atom->cutneighsq[i] = param->cutneigh * param->cutneigh;
atom->cutforcesq[i] = param->cutforce * param->cutforce;
}
fprintf(stdout, "Read %d atoms from %s\n", natoms, param->input_file);
return natoms;
}
void growAtom(Atom *atom) void growAtom(Atom *atom)
{ {
int nold = atom->Nmax; int nold = atom->Nmax;

4
src/eam_utils.c
View File

@ -43,7 +43,7 @@ void initEam(Eam* eam, Parameter* param) {
} }
void coeff(Eam* eam, Parameter* param) { void coeff(Eam* eam, Parameter* param) {
read_file(&eam->file, param->input_file); read_eam_file(&eam->file, param->eam_file);
param->mass = eam->file.mass; param->mass = eam->file.mass;
param->cutforce = eam->file.cut; param->cutforce = eam->file.cut;
param->cutneigh = param->cutforce + 1.0; param->cutneigh = param->cutforce + 1.0;
@ -59,7 +59,7 @@ void init_style(Eam* eam, Parameter* param) {
array2spline(eam, param); array2spline(eam, param);
} }
void read_file(Funcfl* file, const char* filename) { void read_eam_file(Funcfl* file, const char* filename) {
FILE* fptr; FILE* fptr;
char line[MAXLINE]; char line[MAXLINE];

1
src/includes/atom.h
View File

@ -41,6 +41,7 @@ typedef struct {
extern void initAtom(Atom*); extern void initAtom(Atom*);
extern void createAtom(Atom*, Parameter*); extern void createAtom(Atom*, Parameter*);
extern int readAtom(Atom*, Parameter*);
extern void growAtom(Atom*); extern void growAtom(Atom*);
#ifdef AOS #ifdef AOS

2
src/includes/eam.h
View File

@ -47,7 +47,7 @@ typedef struct {
void initEam(Eam* eam, Parameter* param); void initEam(Eam* eam, Parameter* param);
void coeff(Eam* eam, Parameter* param); void coeff(Eam* eam, Parameter* param);
void init_style(Eam* eam, Parameter *param); void init_style(Eam* eam, Parameter *param);
void read_file(Funcfl* file, const char* filename); void read_eam_file(Funcfl* file, const char* filename);
void file2array(Eam* eam); void file2array(Eam* eam);
void array2spline(Eam* eam, Parameter* param); void array2spline(Eam* eam, Parameter* param);
void interpolate(int n, MD_FLOAT delta, MD_FLOAT* f, MD_FLOAT* spline); void interpolate(int n, MD_FLOAT delta, MD_FLOAT* f, MD_FLOAT* spline);

2
src/includes/neighbor.h
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@ -34,7 +34,7 @@ typedef struct {
} Neighbor; } Neighbor;
extern void initNeighbor(Neighbor*, Parameter*); extern void initNeighbor(Neighbor*, Parameter*);
extern void setupNeighbor(); extern void setupNeighbor(Parameter*);
extern void binatoms(Atom*); extern void binatoms(Atom*);
extern void buildNeighbor(Atom*, Neighbor*); extern void buildNeighbor(Atom*, Neighbor*);
extern void sortAtom(Atom*); extern void sortAtom(Atom*);

2
src/includes/parameter.h
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@ -51,7 +51,9 @@ typedef struct {
MD_FLOAT cutneigh; MD_FLOAT cutneigh;
int nx, ny, nz; int nx, ny, nz;
MD_FLOAT lattice; MD_FLOAT lattice;
MD_FLOAT xlo, xhi, ylo, yhi, zlo, zhi;
MD_FLOAT xprd, yprd, zprd; MD_FLOAT xprd, yprd, zprd;
double proc_freq; double proc_freq;
char* eam_file;
} Parameter; } Parameter;
#endif #endif

20
src/main.c
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@ -88,13 +88,17 @@ double setup(
S = getTimeStamp(); S = getTimeStamp();
initAtom(atom); initAtom(atom);
initNeighbor(neighbor, param);
initPbc(atom); initPbc(atom);
initStats(stats); initStats(stats);
setupNeighbor(); initNeighbor(neighbor, param);
createAtom(atom, param); if(param->input_file == NULL) {
createAtom(atom, param);
} else {
readAtom(atom, param);
}
setupNeighbor(param);
setupThermo(param, atom->Natoms); setupThermo(param, atom->Natoms);
adjustThermo(param, atom); if(param->input_file == NULL) { adjustThermo(param, atom); }
setupPbc(atom, param); setupPbc(atom, param);
updatePbc(atom, param); updatePbc(atom, param);
buildNeighbor(atom, neighbor); buildNeighbor(atom, neighbor);
@ -209,6 +213,11 @@ int main(int argc, char** argv)
param.input_file = strdup(argv[++i]); param.input_file = strdup(argv[++i]);
continue; continue;
} }
if((strcmp(argv[i], "-e") == 0))
{
param.eam_file = strdup(argv[++i]);
continue;
}
if((strcmp(argv[i], "-n") == 0) || (strcmp(argv[i], "--nsteps") == 0)) if((strcmp(argv[i], "-n") == 0) || (strcmp(argv[i], "--nsteps") == 0))
{ {
param.ntimes = atoi(argv[++i]); param.ntimes = atoi(argv[++i]);
@ -244,7 +253,8 @@ int main(int argc, char** argv)
printf("MD Bench: A minimalistic re-implementation of miniMD\n"); printf("MD Bench: A minimalistic re-implementation of miniMD\n");
printf(HLINE); printf(HLINE);
printf("-f <string>: force field (lj or eam), default lj\n"); printf("-f <string>: force field (lj or eam), default lj\n");
printf("-i <string>: input file for EAM\n"); printf("-i <string>: input file with atom positions (dump)\n");
printf("-e <string>: input file for EAM\n");
printf("-n / --nsteps <int>: set number of timesteps for simulation\n"); printf("-n / --nsteps <int>: set number of timesteps for simulation\n");
printf("-nx/-ny/-nz <int>: set linear dimension of systembox in x/y/z direction\n"); printf("-nx/-ny/-nz <int>: set linear dimension of systembox in x/y/z direction\n");
printf("--freq <real>: processor frequency (GHz)\n"); printf("--freq <real>: processor frequency (GHz)\n");

38
src/neighbor.c
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@ -71,22 +71,46 @@ void initNeighbor(Neighbor *neighbor, Parameter *param)
neighbor->neighbors = NULL; neighbor->neighbors = NULL;
} }
void setupNeighbor() void setupNeighbor(Parameter* param)
{ {
MD_FLOAT coord; MD_FLOAT coord;
int mbinxhi, mbinyhi, mbinzhi; int mbinxhi, mbinyhi, mbinzhi;
int nextx, nexty, nextz; int nextx, nexty, nextz;
if(param->input_file != NULL) {
xprd = param->xprd;
yprd = param->yprd;
zprd = param->zprd;
}
// TODO: update lo and hi for standard case and use them here instead
MD_FLOAT xlo = 0.0; MD_FLOAT xhi = xprd; MD_FLOAT xlo = 0.0; MD_FLOAT xhi = xprd;
MD_FLOAT ylo = 0.0; MD_FLOAT yhi = yprd; MD_FLOAT ylo = 0.0; MD_FLOAT yhi = yprd;
MD_FLOAT zlo = 0.0; MD_FLOAT zhi = zprd; MD_FLOAT zlo = 0.0; MD_FLOAT zhi = zprd;
cutneighsq = cutneigh * cutneigh; cutneighsq = cutneigh * cutneigh;
binsizex = xprd / nbinx;
binsizey = yprd / nbiny; if(param->input_file != NULL) {
binsizez = zprd / nbinz; binsizex = cutneigh * 0.5;
bininvx = 1.0 / binsizex; binsizey = cutneigh * 0.5;
bininvy = 1.0 / binsizey; binsizez = cutneigh * 0.5;
bininvz = 1.0 / binsizez; nbinx = (int)((param->xhi - param->xlo) / binsizex);
nbiny = (int)((param->yhi - param->ylo) / binsizey);
nbinz = (int)((param->zhi - param->zlo) / binsizez);
if(nbinx == 0) { nbinx = 1; }
if(nbiny == 0) { nbiny = 1; }
if(nbinz == 0) { nbinz = 1; }
bininvx = nbinx / (param->xhi - param->xlo);
bininvy = nbiny / (param->yhi - param->ylo);
bininvz = nbinz / (param->zhi - param->zlo);
} else {
binsizex = xprd / nbinx;
binsizey = yprd / nbiny;
binsizez = zprd / nbinz;
bininvx = 1.0 / binsizex;
bininvy = 1.0 / binsizey;
bininvz = 1.0 / binsizez;
}
coord = xlo - cutneigh - SMALL * xprd; coord = xlo - cutneigh - SMALL * xprd;
mbinxlo = (int) (coord * bininvx); mbinxlo = (int) (coord * bininvx);

47
src/util.c
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@ -30,13 +30,50 @@
#define IR 2836 #define IR 2836
#define MASK 123459876 #define MASK 123459876
double myrandom(int* idum) double myrandom(int* seed)
{ {
int k= (*idum) / IQ; int k= (*seed) / IQ;
double ans; double ans;
*idum = IA * (*idum - k * IQ) - IR * k; *seed = IA * (*seed - k * IQ) - IR * k;
if(*idum < 0) *idum += IM; if(*seed < 0) *seed += IM;
ans = AM * (*idum); ans = AM * (*seed);
return ans; return ans;
} }
void random_reset(int *seed, int ibase, double *coord)
{
int i;
char *str = (char *) &ibase;
int n = sizeof(int);
unsigned int hash = 0;
for (i = 0; i < n; i++) {
hash += str[i];
hash += (hash << 10);
hash ^= (hash >> 6);
}
str = (char *) coord;
n = 3 * sizeof(double);
for (i = 0; i < n; i++) {
hash += str[i];
hash += (hash << 10);
hash ^= (hash >> 6);
}
hash += (hash << 3);
hash ^= (hash >> 11);
hash += (hash << 15);
// keep 31 bits of unsigned int as new seed
// do not allow seed = 0, since will cause hang in gaussian()
*seed = hash & 0x7ffffff;
if (!(*seed)) *seed = 1;
// warm up the RNG
for (i = 0; i < 5; i++) myrandom(seed);
//save = 0;
}