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Commit bb42a5dd authored by Mark Friedrichs's avatar Mark Friedrichs
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Update for getState()

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examples/HelloArgonInC.c
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/* ----------------------------------------------------------------------------- Vim: Warning: Output is not to a terminal
* OpenMM(tm) HelloArgon example in C (June 2009) [?1049h[?1h=[?12;25h[?12l[?25h[?25l"svn-commit.2.tmp" 5L, 119C 1
* ----------------------------------------------------------------------------- 2 --This line, and those below, will be ignored--
* This program demonstrates a simple molecular simulation using the OpenMM  3
* API for GPU-accelerated molecular dynamics simulation. The primary goal is 4 M examples/HelloArgonInC.c
* to make sure you can compile, link, and run with OpenMM and view the output.  5 M examples/HelloSodiumChlorideInC.c
* The example is available in C++, C, and Fortran 95. ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ 1,0-1All[?12l[?25h[?25l2,1 [?12l[?25h[?25l1,0-1[?12l[?25h[?25l-- INSERT --1,1All[?12l[?25h[?25lM2[?12l[?25h[?25l1[?12l[?25h[?25lU2[?12l[?25h[?25lp3[?12l[?25h[?25ld4[?12l[?25h[?25la5[?12l[?25h[?25lt6[?12l[?25h[?25le7[?12l[?25h[?25l8[?12l[?25h[?25lf9[?12l[?25h[?25lo10[?12l[?25h[?25lr1[?12l[?25h[?25l2[?12l[?25h[?25lg3[?12l[?25h[?25le4[?12l[?25h[?25lt5[?12l[?25h[?25lS6[?12l[?25h[?25lt7[?12l[?25h[?25la8[?12l[?25h[?25lt9[?12l[?25h[?25le20[?12l[?25h[?25l(1[?12l[?25h[?25l)0[?12l[?25h[?25l()1,21All[?12l[?25h[?25l:[?12l[?25hwq[?25l"svn-commit.2.tmp" 5L, 140C written
* [?1l>[?12l[?25h[?1049lSending examples/HelloArgonInC.c
* The system modeled here is a small number of argon atoms in a vacuum. Sending examples/HelloSodiumChlorideInC.c
* A multi-frame PDB file is written to stdout which can be read by VMD or
* other visualization tool to produce an animation of the resulting trajectory.
* -------------------------------------------------------------------------- */
#include "OpenMMCWrapper.h"
#include <stdio.h>
/* Forward declaration of routine for printing one frame of the
trajectory, defined later in this source file. */
void writePdbFrame(int frameNum, const OpenMM_State*);
void simulateArgon()
{
OpenMM_System* system;
OpenMM_Integrator* integrator;
OpenMM_Context* context;
OpenMM_Platform* platform;
OpenMM_NonbondedForce* nonbond;
OpenMM_Vec3Array* initPosInNm;
OpenMM_StringArray* pluginList;
int a, frameNum;
/* Load any shared libraries containing GPU implementations. */
pluginList = OpenMM_Platform_loadPluginsFromDirectory(
OpenMM_Platform_getDefaultPluginsDirectory());
OpenMM_StringArray_destroy(pluginList);
/* Create a system with nonbonded forces. System takes ownership
of Force; don't destroy it yourself. */
system = OpenMM_System_create();
nonbond = OpenMM_NonbondedForce_create();
OpenMM_System_addForce(system, (OpenMM_Force*)nonbond);
/* Create three atoms. */
initPosInNm = OpenMM_Vec3Array_create(3);
for (a = 0; a < 3; ++a)
{
const OpenMM_Vec3 posNm = {0.5*a, 0, 0}; /*location, nm*/
OpenMM_Vec3Array_set(initPosInNm, a, posNm);
OpenMM_System_addParticle(system, 39.95); /*mass of Ar, grams/mole*/
/* charge, L-J sigma (nm), well depth (kJ) */
OpenMM_NonbondedForce_addParticle(nonbond, 0.0, 0.3350, 0.996); /*vdWRad(Ar)=.188 nm*/
}
/* Create particular integrator, and recast to generic one. */
integrator = (OpenMM_Integrator*)OpenMM_VerletIntegrator_create(0.004); /*step size in ps*/
/* Let OpenMM Context choose best platform. */
context = OpenMM_Context_create(system, integrator);
platform = OpenMM_Context_getPlatform(context);
printf( "REMARK Using OpenMM platform %s\n",
OpenMM_Platform_getName(platform));
/* Set starting positions of the atoms. Leave time and velocity zero. */
OpenMM_Context_setPositions(context, initPosInNm);
/* Simulate. */
for (frameNum=1; ;++frameNum) {
/* Output current state information. */
OpenMM_State* state = OpenMM_Context_getState(context, OpenMM_State_Positions, 0);
const double timeInPs = OpenMM_State_getTime(state);
writePdbFrame(frameNum, state); /*output coordinates*/
OpenMM_State_destroy(state);
if (timeInPs >= 10.)
break;
/* Advance state many steps at a time, for efficient use of OpenMM. */
OpenMM_Integrator_step(integrator, 10); /*(use a lot more than this normally)*/
}
/* Free heap space for all the objects created above. */
OpenMM_Vec3Array_destroy(initPosInNm);
OpenMM_Context_destroy(context);
OpenMM_Integrator_destroy(integrator);
OpenMM_System_destroy(system);
}
int main()
{
simulateArgon();
return 0;
}
/* Handy homebrew PDB writer for quick-and-dirty trajectory output. */
void writePdbFrame(int frameNum, const OpenMM_State* state)
{
int a;
/* Reference atomic positions in the OpenMM State. */
const OpenMM_Vec3Array* posInNm = OpenMM_State_getPositions(state);
/* Use PDB MODEL cards to number trajectory frames. */
printf("MODEL %d\n", frameNum); /*start of frame*/
for (a = 0; a < OpenMM_Vec3Array_getSize(posInNm); ++a)
{
OpenMM_Vec3 posInAng;
/* "10" here converts nanometers to Angstroms */
posInAng = OpenMM_Vec3_scale(*OpenMM_Vec3Array_get(posInNm, a), 10.);
printf("ATOM %5d AR AR 1 ", a+1); /*atom number*/
printf("%8.3f%8.3f%8.3f 1.00 0.00\n", /*coordinates*/
posInAng.x, posInAng.y, posInAng.z);
}
printf("ENDMDL\n"); /*end of frame*/
}
......
examples/HelloSodiumChlorideInC.c
View file @ bb42a5dd
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