/usr/share/libavogadro/shaders/phong.frag is in avogadro-data 1.2.0-1+deb9u1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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//
// Do one per fragment diffuse light
// + four specular lights
// + four more specular lights
// 8 specular lights per fragment!
const float Shininess = 40.0;
void main (void)
{
//
// vec3 EyeNormal = vec3(gl_TexCoord0);
//
// vec3 ULLight = vec3(gl_TexCoord1);
// vec3 LRLight = vec3(gl_TexCoord2);
// vec3 RimLight = vec3(gl_TexCoord3);
//
// vec4 DifColor = vec4(gl_TexCoord4);
// vec4 SpecColor = vec4(gl_TexCoord5);
// vec4 ULColor = vec4(gl_TexCoord6);
// vec4 LRColor = vec4(gl_TexCoord7);
//
vec3 NNormal;
vec3 LNormal;
vec4 MyColor;
vec4 SpecularColor;
float Intensity;
//
// Since the normal is getting interpolated, we
// have to first restore it by normalizing it.
//
// NNormal = normalize( EyeNormal );
NNormal = normalize( vec3(gl_TexCoord[0]) );
//
// Per fragment diffuse lighting
// We are going to put the diffuse light about
// the right spot....
////// Intensity = dot ( ULLight, NNormal );
Intensity = dot (vec3(gl_TexCoord[1]), NNormal );
Intensity = max ( Intensity, 0.0 );
////// MyColor = vec4(Intensity) * DifColor;
MyColor = vec4(Intensity) * gl_TexCoord[4];
//
// We are going to point the normal to the
// upper right front all of the time by taking
// the abs. No need to normalize again.
//
NNormal = abs(NNormal);
//
// Now, start the specular calculations.
//
////// Intensity = dot( NNormal, LRLight );
Intensity = dot( NNormal, vec3( gl_TexCoord[1] ) );
Intensity = max( Intensity, 0.0 );
Intensity = pow( Intensity, Shininess );
////// MyColor += vec4(Intensity) * ULColor;
MyColor += vec4(Intensity) * gl_TexCoord[6];
////// Intensity = dot( NNormal, LRLight );
Intensity = dot( NNormal, vec3( gl_TexCoord[2] ) );
Intensity = max( Intensity, 0.0 );
Intensity = pow( Intensity, Shininess );
////// MyColor += vec4(Intensity) * ULColor;
MyColor += vec4(Intensity) * gl_TexCoord[7];
//
// Squash the Y of the normal vector
//
NNormal.y = 0.0;
NNormal = normalize( NNormal );
////// Intensity = dot( NNormal, RimLight );
Intensity = dot( NNormal, vec3( gl_TexCoord[3] ) );
////// Intensity = max( Intensity, 0.0 );
Intensity = pow( Intensity, Shininess );
////// MyColor += vec4(Intensity) * SpecColor;
MyColor += vec4(Intensity) * gl_TexCoord[5];
////// MyColor.a = Difcolor.a;
MyColor.a = gl_TexCoord[4].a;
gl_FragColor = MyColor;
}
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